University of California, San Francisco

CURRICULUM VITAE

Name:

Andrej Sali, PhD

Position:	Professor, Step A/S
	Bioengineering & Therapeutic Sciences
	School of Pharmacy

Address:	Box 2552 1700 4th Street, 503B University of California, San Francisco San Francisco, CA 94158
	Voice: 514-4227
	Fax: 514-4231
	Email: sali@salilab.org

EDUCATION

1983 - 1987	University of Ljubljana, Slovenia	BSC	Chemistry
1987 - 1991	University of London, UK	PhD	Molecular Biophysics

PRINCIPAL POSITIONS HELD

1987 - 1991	Birkbeck College, and Imperial Cancer Research Fund, London, UK. (Mentor: Prof. Thomas L. Blundell, FRS).	PhD student	Crystallography
1991 - 1994	Harvard University, Cambridge, USA. (Mentor: Prof. Martin Karplus).	Postdoctoral Fellow	Chemistry
1995 - 2000	The Rockefeller University	Assistant Professor
2000 - 2003	The Rockefeller University	Associate Professor
2003 - present	University of California, San Francisco	Professor	Department of Bioengineering and Therapeutic Sciences

OTHER POSITIONS HELD CONCURRENTLY

2009 - 2012	California Institute for Quantitative Biosciences (QB3) at UCSF	Director
2003 - 2015	UCSF	Vice Chair	Department of Bioengineering and Therapeutic Sciences
2003 - present	California Institute for Quantitative Biosciences (QB3)	Faculty Member
2003 - present	UCSF	Faculty Member	Pharmaceutical Sciences and Pharmacogenomics Graduate Program
2003 - present	UCSF	Faculty Member	Biophysics Graduate Program
2003 - present	UCSF	Faculty Member	Bioinformatics and Medical Informatics Graduate Program
2003 - present	UCSF	Faculty Member	Chemistry and Chemical Biology Graduate Program
2015 - 2023	School of Pharmacy, UCSF	Associate Dean for Research

HONORS AND AWARDS

1984	Undergraduate scholarship	J. Stefan Institute, Ljubljana, Slovenia.
1985	British Council Visiting Student	Birkbeck College, London, UK.
1987	British Council Visiting Student	Birkbeck College, London, UK.
1987	Overseas Research Students Award (1987-1990)	Committee of Principals and Vice Chancellors, England.
1987	Scholarship for graduate studies (1987-1988)	Research Council of Slovenia.
1989	Academic Scholarship (1989-1990)	Merck Sharp & Dohm
1991	Postdoctoral Fellow (1991-1994)	Jane Coffin Childs Memorial Fund for Medical Research
1996	Alexandrine and Alexander L. Sinsheimer Scholar (1996-1999)	Alexandrine and Alexander L. Sinsheimer Foundation
1998	Alfred P. Sloan Research Fellow (1998-2000)	Alfred P. Sloan Foundation
2000	Irma T. Hirschl Career Award Scientist (2000-2003)	Irma T. Hirschl Foundation
2007	Zois Award, Science Ambassador	Republic of Slovenia
2014	Fellow	International Society for Computational Biology (ISCB)
2015	Apple Teaching Award	School of Pharmacy, UCSF
2017	Academy Jubilee Professorship	Indian Academy of Sciences
2018	Bijvoet Medal	Utrecht University, Netherlands
2018	Member	National Academy of Sciences, USA
2023	Jack Peter Green Lecture	Mount Sinai School of Medicine, New York City
2024	Basic Faculty Research Lecture	UCSF, San Francisco

KEYWORDS/AREAS OF INTEREST

Structural biology, computational biology, bioinformatics, proteins, macromolecular complexes, assemblies, macromolecular processes, sequence, structure, function, evolution, modeling of protein structure, prediction of protein function.

We develop, apply, and disseminate integrative spatiotemporal modeling methods to facilitate biological and biomedical discovery.

PROFESSIONAL ACTIVITIES

MEMBERSHIPS

1991 - present	Protein Society
1991 - present	American Association for the Advancement of Science
2007 - present	Biophysical Society
2014 - present	International Society for Computational Biology

SERVICE TO PROFESSIONAL ORGANIZATIONS

2005 - 2008	Protein Society	Executive Committee
2005 - present	Protein Data Bank	Scientific Advisory Committee
2009 - 2013	PROSPECTS (Proteomics Specification in Time and Space) consortium	Scientific Advisory Committee
2010 - 2010	Keystone Symposia	Scientific Advisory Board (ad hoc)
2011 - 2015	Keystone Symposia	Scientific Advisory Board
2010 - present	Protein Data Bank	Electron Microscopy Validation Task Force (Co-Chair)
2010 - present	Protein Data Bank	Small Angle Scattering Task Force
2014 - present	Protein Data Bank	Hybrid Models Task Force (Co-Chair)
2010 - present	Electron Microscopy Data Bank	Scientific Advisory Committee
2009 - present	PSI Knowledgebase	Working Group on Theoretical Structural Model Validation
2011 - present	Rosetta Commons	Scientific Advisory Board
2017 - 2019	Biophysical Society	Committee member of BPS
2022 - 2025	Advanced Light Source at LBNL	Scientific Advisory Committee

SERVICE TO PROFESSIONAL PUBLICATIONS

2003 - 2021	Editor, Structure.
2018 - present	Editorial Board, Proceedings of National Academy of Sciences, USA
2004 - present	Editorial Board, PLoS Computational Biology.
2002 - present	Editorial Board, Journal of Computer Aided Molecular Design.
2002 - present	Editorial Board, Molecular and Cellular Proteomics.
2004 - present	Editorial Board, Protein Engineering, Design, and Selection.
2001 - present	Section Head for the Structural Genomics section on BioMed Central
1990 - present	Reviewer for Nature, Science Cell, Proc. Natl. Acad. Sci. USA, Nature Structural and Molecular Biology Nature Genetics, Nature Biotechnology, Structure, Journal of Molecular Biology, Proteins, Protein Engineering, Design, and Selection, Protein Science, Bioinformatics, Nucleic Acids Research, Journal of Biological Chemistry, BMC Structural Biology, Genome Biology, FEBS Letters, Journal of Computer Aided Molecular Design, Biophysical Journal, Biochemical Journal, PLoS Biology, and PLoS Computational Biology.

INVITED PRESENTATIONS - INTERNATIONAL

1999	CERCA CADD Symposium, Montreal, Canada. April 13, 1999.
1999	Data Mining in Crystallography, Erice, Italy. May 15, 1999.
1999	Structural Biology Net, Tallberg, Sweden. June, 1999.
1999	Frontiers in Structural Biology, Indian Institute of Science, Bangalore, India. August 27, 1999.
1999	BRI, Montreal, Canada. November 24, 1999.
1999	University of Toronto, Toronto, Canada. December 9, 1999.
2000	Japan Biophysical Society Meeting, Tokyo, Japan. January 17, 2000.
2000	Bioinformatics 2000, Elsinore, Denmark. April 28, 2000.
2001	University of Zuerich, Zuerich, Switzerland. December 5, 2001.
2001	Bioinformatics & Proteomics: From Sequence to Function, Lausanne, Switzerland. December 6, 2001.
2001	Structural Genomics and Bioinformatics, Instituto Juan March, Madrid, Spain. March 12-14, 2001.
2001	Annual meeting of the Canadian Society for Biochemistry and Molecular and Cellular Biology (CSBMCB), Toronto, Canada. May 31-June 3, 2001.
2001	Math/Chem/Comp 2001, Dubrovnik, Croatia. June 25-30, 2001.
2001	4th International Conference on Biological Physics, ICBP2001, Kyoto, Japan. July 30-August 3, 2001.
2001	4th International Conference on Molecular Structural Biology, ICMSB2001, Vienna, Austria. September 5-9, 2001.
2001	Genomics & Proteomics meeting, Barcelona, Spain. October 19, 2001.
2002	University of Barcelona, Barcelona, Spain. May 21, 2002.
2002	Genomics & Proteomics meeting, Barcelona, Spain. May 22, 2002.
2002	Samuel Lunenfeld Research Institute, Toronto, Canada. May 29, 2002.
2002	The 19th Congress and General Assembly of the International Union of Crystallography IUCR, Geneva, Switzerland. August 6-15, 2002.
2002	Genomics and Bioinformatics Center Inaugural Symposium, Pontificia Universidad Catolica, Santiago, Chile. November 18-20, 2002.
2003	Fourteenth Annual World Molecular Engineering Network (WMEN) Conference, San Jose del Cabo, Baja California Sur, Mexico. May 4-8, 2003.
2003	5th Meeting of the Slovenian Biochemical Society, Ljubljana, Slovenia. September 24-28, 2003.
2004	University of Cologne, Cologne, Germany. January 19, 2004.
2004	Ringberg meeting, Schloss Ringberg, Germany. January 21-23, 2004.
2004	Fourteenth Annual World Molecular Engineering Network (WMEN) Conference (2004), San Jose del Cabo, Baja California Sur, Mexico. May 2-6, 2004.
2004	EMBO conference on Structures in Biology, EMBL, Heidelberg, Germany. November 10-13, 2004.
2005	The 7th World Congress of the World Association of Theoretically Oriented Chemists (WATOC), Capetown, South Africa. January 16-21, 2005.
2005	Keynote Speaker in XX IUCr Congress in Firenze, Italy. August 23-31, 2005.
2005	Speaker at the International Workshop M2CELL, The Royal Abbey of Fontevraud, Paris, France. December 4-6, 2005.
2006	Organizer and Speaker at the World Molecular Engineering Network Conference. Cabo San Lucas, Mexico. April 30-May 2nd, 2006.
2006	Plenary Speaker at the 11th Symposium on Recent Advances in Biophysics, National Taiwan University, Taipei, Taiwan. May 23-26, 2006
2006	2006 Keystone Symposium on Multi-Protein Complexes Involved in Cell Regulation, St. John's College, Cambridge, UK. August 18-23, 2006.
2007	Organizer and Speaker at the World Molecular Engineering Network Conference. Cabo San Lucas, Mexico. April 29-May 2nd, 2007.
2007	Protein Complexes and Protein Networks Symposium in Martinsried, Germany, May 21-22, 2007.
2007	Symposium on Structural Biology and its Application to Drug Development at the University of Tokyo, Tokyo, Japan, 28 January 2007.
2008	Invited Speaker at the Basel Computational Biology Conference [BC]2 , Basel, Switzerland, March 13-14, 2008.
2008	Organizer and Speaker of the World Molecular Engineering Network Conferenc. Cabo San Lucas, Mexico. May 4-8, 2008.
2008	University of Toronto, Canada, 26 July, 2008.
2008	Speaker at the 40th Course: From Molecules to Medicines Integrating Crystallography in Drug Discovery, Erice, Italy. May 29 - June 8, 2008.
2008	Speaker at the Gordon Research Conference on Macromolecular Organization & Cell Function: Systems Cell Biology, Oxford, England, July 27 to August 2, 2008.
2008	Speaker at the 6th National NCCR Symposium on New Trends in Structural Biology, Zurich, Switzerland, September 8-9 2008.
2008	Speaker at the Max Planck Institute, Student Workshop, Goettingen, Germany. September 10-13 2008.
2008	Speaker at the Max Planck Institute of Biochemistry, INSTRUCT Open Meeting, in Martinsried, Germany, October 16-17 2008.
2009	Speaker at the NoE 3DEM final Meeting, Brdo, Slovenia, February 9-13, 2009.
2009	McDowell Lecture at the University of British Columbia, Vancouver, BC, Canada, March 10, 2009.
2009	Seminar at the University of Ljubljana, Ljubljana, Slovenia, December 17, 2009.
2010	Organizer and Speaker at the 20th World Molecular Engineering Network Conference, Cabo San Lucas, Mexico, May 2-5, 2010.
2010	Speaker at the Institute of Structural Molecular Biology, Birkbeck Institute, London, England, June 17-18, 2010
2010	Speaker at the MPIMP Dahlem Colloquia in Molecular Genetics, Max Planck Institute, Berlin, Germany, August 22-24, 2010.
2010	Speaker at Exeter College, Oxford University, England, October 4, 2010.
2010	Speaker at the PROteomics SPECification in Time and Space - PROSPECTS Meeting, Taormina, Sicily, Italy, November 2-4, 2010.
2010	Speaker at the 6th International Conference on Structural Biology and Functional Genomics, National University of Singapore, Singapore, December 6-8, 2010.
2011	Organizer and Speaker at the 21st World Molecular Engineering Network Conference, Cabo San Lucas, Mexico, May 1-4, 2011.
2011	Speaker at the International Conference on Structural Genomics, University of Toronto, Toronto, Ontario, Canada, May 10-14, 2011.
2011	Speaker at IGBMC, Strasbourg, France, July 17-18, 2011.
2011	Speaker at Max Planck Institute, Munich, Germany, July 20-21, 2011.
2011	Plenary Speaker at the ComBio 2011, Cairns Convention Centre, Cairns, Australia, September 26-29, 2011.
2012	Plenary Speaker at the Molecular Modeling Meeting, Queenstown, New Zealand, August 30-September 1, 2012.
2013	Speaker at the Swiss Federal Institute of Technology, Lausanne, Switzerland, January 14, 2013.
2013	Speaker at the Biozentrum Lecture, Basel, Switzerland, January 15, 2013.
2013	Organizer and Speaker at the 23rd World Molecular Engineering Network Conference, Cabo San Lucas, Mexico, May 5-8, 2013.
2013	Speaker at the Bioinformatics Meeting, Recife, Brazil, November 3-7, 2013.
2014	Speaker at the Lorne Conference, Victoria, Australia, February 9-13, 2014.
2014	Speaker at Shanghai Tech University, Shanghai, China, March 14-18, 2014
2014	Organizer and Speaker at the 24th World Molecular Engineering Network Conference, Cabo San Lucas, Mexico, May 4-7, 2014
2014	Keynote Speaker at the Emerging Trends in Computational Biology Conference, Singapore, June 20-21, 2014
2014	Speaker at the PDB Hybrid Methods Task Force Meeting, EMBL-EBI, HInxton, UK, October 6-7, 2014
2015	Seminar at A*Star BII, Singapore, March 12-14, 2015
2015	Organizer and Speaker at the 25th World Molecular Engineering Network Conference, Cabo San Lucas, Mexico, May 3-6, 2015
2015	Speaker at the GRC on Computational Aspects of Biomolecular NMR, Il Ciocco, Italy, June 7-12, 2015
2015	Speaker at the 29th Annual Symposium of the Protein Society, Barcelona, Spain, July 22-25, 2015
2015	Seminar at Pasteur Institute, Paris, June 24, 2015
2015	Speaker at iHuman Institute, Shanghai Tech University, Shanghai, China, July 27-31, 2015
2015	Keynote Speaker at the FEBS3+ Meeting "Molecules of Life", Portoroz, Slovenia, September 16-19, 2015.
2015	Speaker at the Hybrid Methods Meeting, Osaka, Japan, October 2-4, 2015
2015	Speaker at the Advances in Integrative Biology of Cellular Processes, Shanghai, China, November 10-12, 2015.
2016	Speaker at the Graduate School of Quantitative Biosciences Munich (QBM), Munich, Germany, January 11, 2016.
2016	Speaker at the EMBL Distinguished Lecture Series, Heidelberg, Germany, January 12, 2016.
2016	Organizer and Speaker at the 26th World Molecular Engineering Network Conference, Cabo San Lucas, Mexico, May 7-10, 2016.
2016	Speaker at the ETH Zurich Department of Biology Symposium, Zurich, Switzerland, June 13-15, 2016.
2016	Speaker at the Max F. Perutz Laboratories, The IMP, Vienna, Austria, June 28-29, 2016.
2017	Speaker at the Bioimaging Data Repositories Workshop, EMBL-EBI, Hinxton, UK, Jan 23-24, 2017.
2017	Speaker at the Frontiers of NMR in Life Sciences, Keystone, CO, March 12-17, 2017.
2017	Organizer and Speaker at the 27th World Molecular Engineering Network Conference, Cabo San Lucas, Mexico, May 6-9, 2017.
2017	Seminar at the Sophia College for Women, Mumbai, Jul 24, 2017.
2017	Seminar at the Tata Institute for Fundamental Research, Mumbai, Jul 24, 2017.
2017	Seminar at the Dept. of Chemistry, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, Jul 26, 2017.
2017	Seminar at the Ahmednagar College, Ahmednagar, Jul 28, 2017.
2017	Seminar at the Indian Institute of Science Education and Research, Pune, Jul 31, 2017.
2017	Seminar at the Institute of Bioinformatics and Biotechnology, Pune University, Pune, Aug 1, 2017.
2017	Seminar at the National Center for Biological Sciences, Bangalore, Aug 2, 2017.
2017	Seminar at the Indian Institute of Sciences, Bangalore, Aug 3, 2017.
2017	Seminar at the Mysore College, Mysore, Aug 4, 2017.
2017	Seminar at the Molecular Biophysics Unit, Indian Institute of Sciences, Bangalore, Aug 7, 2017.
2017	Speaker at the Conformational ensembles from experimental data and computer simulations, Biophysical Society, Berlin, Germany, Aug 25-29, 2017.
2017	Speaker at the QBI 2017 Cell Mapping Symposium, UCSF, San Francisco, CA, Sep 13-14, 2017.
2017	Speaker at the iHuman Institute at ShanghaiTech Symposium, Shanghai, China, Nov 7-8, 2017.
2017	Speaker at the EMBL/EMBO Symposium: From Single- to Multiomics: Applications and Challenges Data Integration, Heidelberg, Germany, November 12-14, 2017.
2017	Speaker at the Revolutions in Structural Biology: Celebrating the 100th anniversary of Sir John Kendrew, EMBL, Heidelberg, Germany, Nov 16-17, 2017.
2018	Speaker at the 3rd DNA Replication and Repair Structures & Cancer Conference, Cancun, Mexico, Feb 11-15, 2018.
2018	Keynote Speaker at the 2018 Annual Symposium of the Bijvoet Center of Biomolecular Research, Utrecht, Netherlands, Apr 23-24, 2018.
2018	Organizer and Speaker at the 28th World Molecular Engineering Network Conference, Cabo San Lucas, Mexico, May 5-8, 2018.
2019	Organizer of the 63rd Annual Meeting of the Biophysical Society, Baltimore, MD, Mar 2-6, 2019.
2019	Speaker at the ACS Annual Meeting, Orlando, Florida, March 30, 2019.
2019	Organizer and Speaker at the 29th World Molecular Engineering Network Conference, Cabo San Lucas, Mexico, May 4-7, 2019.
2019	Speaker at the INSTRUCT Biennial Meeting, Madrid, Spain, May 22, 2019.
2019	Speaker at the QBI FU Berlin Meeting, Berlin, Germany, May 26, 2019.
2019	Speaker at the EMBL Multiomics Meeting, Heidelberg, Germany, September 11, 2019.
2019	Speaker at the Structural Proteomics Meeting, Goettingen, Germany, November 3, 2019.
2019	Speaker at the TAU QBI Meeting, Tel Aviv, Israel, December 4, 2019.
2019	Speaker at the iHuman Institute, ShanghaiTech, Shanghai, China, December 18, 2019.
2020	Speaker, G.N. Ramachandran Memorial Lecture at the Indian Biophysical Society 2020 Meeting, Mumbai, India, March 12, 2020.
2020	Speaker at the EMBL Conference: In situ Structural Biology - From Cryo-EM to Integrative Modelling, Heidelberg, Germany, December 6-8, 2020.
2021	Speaker at the Workshop on Strategy for future EMBL research infrastructures in the Life Sciences in Hamburg, Hamburg, Germany, April 19-20, 2021.
2021	Seminar at the Basel University, Basel, Switzerland, May 17, 2021.
2021	Speaker at the 2021 ACA Meeting Transactions Symposium, Function Follows Form: Celebrating the 50th Anniversary of the Protein Data Bank”, Baltimore, MD, July 31, 2021.
2021	Speaker at the XXV IUCr Congress Satellite Meeting on “Macromolecular Machines in Biomedicine: Structure, Dynamics, and Evolution”, Prague, Czech Republic, August 21-22, 2021.
2021	Seminar at the Bioinformatics Institute, ASTAR, Singapore, September 2, 2021.
2021	Speaker at the CECAM Workshop: Quantifying Protein Dynamics and Allosteric regulation in the cell with emerging technologies: From Cryo-EM and NMR to Multiscale Simulations, Networks and Machine Learning, Lausanne, Switzerland, September 15-17, 2021.
2022	Speaker at the QBI / Crick Institute Symposium on Quantitative Mapping of the Cell, London, UK, January 23-28, 2022.
2022	Organizer and Speaker at the 32nd World Molecular Engineering Network Conference, Cabo San Lucas, Mexico, May 7-10, 2022.
2022	Speaker at the NS184 Nobel Symposia on “Towards characterizing the human 3D-proteome”, Stockholm, Sweden, May 19-22, 2022.
2023	Speaker at the Seeing is believing: imaging the molecular processes of life, EMBL, Heidelberg, Germany October 4-7, 2023.
2023	Seminar at iHuman Institute, Shanghai, China, October 18, 2023.
2023	Seminar at DESY, Hamburg, Germany, December 4, 2023.
2023	Speaker at Computational Structural Biology Conference, Heidelberg, Germany, December 6-9, 2023.
2024	Keynote Speaker at the 3rd MOSBRI Conference, Ljubljana, Slovenia, June 10-13, 2024.
2024	Speaker at the Protein Society Annual Symposium, Vancouver, Canada, July 23-26, 2024.

INVITED PRESENTATIONS - NATIONAL

1999	Second International Georgia Tech Conference in Bioinformatics, Atlanta, Georgia, USA. November 12, 1999.
1999	2.Structural Genomics Targets Workshop, NIH, Washington DC, USA. February 11, 1999.
1999	Advances & Opportunities at the Biology/Math/Computational/Physical Sciences Interface, Rutgers University, New Brunswick, NJ, USA. March 6, 1999.
1999	Mount Sinai School of Medicine, New York, NY, USA. March 19, 1999.
1999	New York Structural Biology Group, New York Academy of Sciences, New York, NY, USA. March 24, 1999.
1999	Columbia University, New York, NY, USA, 1999.
1999	Chemistry Dept., New York University, New York, NY, USA, 1999.
1999	Protein Sequence Structure Function Meeting, UCSF, San Francisco, CA, USA. April 23, 1999.
1999	The Scripps Institute, La Jolla, CA, USA. August 13, 1999.
1999	Mathematical Problems in the Molecular Sciences, Courant Institute, New York, NY, USA. October 10, 1999.
1999	City College of New York, New York, USA. October 20, 1999.
1999	Agouron Pharmaceuticals, San Diego, California, USA. October 28, 1999.
1999	Structural Genomics Conference, ANL, Chicago, Illinois, USA. November 16, 1999.
1999	Structural Genomics and the Pharmaceutical Industry, Princeton, New Jersey, USA. November 18, 1999.
2000	Quantitative Challenges in the Post Genomic Sequence Era, La Jolla Interfaces in Science, San Diego, California, USA. January 12, 2000.
2000	UCSD, Dept of Physics, San Diego, California, USA. January 19, 2000
2000	UCSF, San Francisco, California, USA. January 20, 2000.
2000	Center for Physics and Biology, Rockefeller University,New York, New York, USA. January 24, 2000.
2000	Biological Chemistry Seminar Series, University of Penn, Philadelphia, Pennsylvania, USA. February 17, 2000.
2000	ABRF 2000 ``From Singular to Global Analyses of Biological Systems'', Bellevue, Washington, USA. February 22, 2000.
2000	AAAS conference, Washington DC, USA. March 20, 2000.
2000	Keystone Symposium on Macromolecular Assemblies at Work: Application of Physics, Chemistry, and Mathematics to Biology, Durango, Colorado, USA. March 25, 2000.
2000	Bio2000, Boston, Massachusetts, USA. March 28, 2000
2000	Computational Challenges of the Post Genomic Age, SUN, San Francisco, California, USA. May 12, 2000.
2000	Biopolymers Gordon Conference, Newport, Rhode Island, USA. June 18-22, 2000.
2000	2000 FASEB Summer Research Conference on Protein Folding in the Cell, Saxton River, Vermont, USA. July 22-27, 2000.
2000	Monsanto/Pharmacia lectureship series, Univ. of Saint Louis, Missouri, USA. September 28, 2000.
2000	Workshop on Structural Genomics. NIGMS, Washington DC, USA. October 23, 2000.
2000	Genomics and Bioinformatics, UMD, New Brunswick, New Jersey, USA. November 2, 2000.
2000	University of Minnesota, Minneapolis, Minnesota, USA. November 27, 2000.
2001	Oncogenomics: Dissecting Cancer Through Genome Research, Nature Genetics, Tuscon, Arizona, USA. January 25-27, 2001.
2001	UAB, Birmingham, Alabama, USA. February 26, 2001.
2001	Bard College, New York, USA. April 18, 2001.
2001	Physics/Chemistry. CSUN, Northridge, California, USA. May 2, 2001.
2001	ACS Meeting, Chicago, Illinois, USA. August 26-30, 2001.
2001	University of Maryland, Maryland, USA. October 2, 2001.
2001	Columbia University, New York, New York, USA. October 15, 2001.
2001	Mast Cell Workshop, Bethesda, Maryland, USA. November 26-30, 2001.
2002	Genomics Seminar Series, Skirball Institute, New York, New York, USA. February 6, 2002.
2002	Mining the Human Genome for New Drug Discovery - New Ways of Handling Orphan Targets. NYAS, New York, New York, USA. February 26, 2002.
2002	Biological Processes for New and Innovative Engineering Systems and Applications, ARO workshop, Research Triangle Park, North Carolina, USA. February 26-27, 2002.
2002	New York City Blood Centre, New York, New York, USA. March 7, 2002.
2002	Proteomics - The New Frontiers: Discovery, Separation, Prediction & Modeling, University of Delaware, Newark, Delaware, USA. March 14-15, 2002.
2002	Harvard University, Cambridge, Massachusetts, USA, March 28, 2002.
2002	Molecular Cell Biology and Biochemistry Seminar Series, Virginia Tech, Blacksburg, Virginia, USA. April 5, 2002.
2002	UCSF, San Francisco, California, USA, April 15, 2002.
2002	A Workshop on large biological structures, Asilomar, California, USA. April 20-22, 2002.
2002	SCBMB Program, Baylor College of Medicine, Houston, Texas, USA. May 15, 2002.
2002	50th ASMS conference American Society of Mass Spectrometry, Orlando, Florida, USA. June 2-6, 2002.
2002	The 5th Summer Session of the New York Structural Biology Discussion Group , Cold Spring Harbor Laboratory, New York, USA. June 26, 2002
2002	Berkeley-Stanford summer school for protein crystallography, SSRL, Stanford, California, USA. July 8-12, 2002.
2002	Gordon Conference on Diffraction Methods in Structural Biology, Connecticut College, New London, Connecticut, USA. July 14-19, 2002.
2002	NYCBS New York Computational Biology Society seminar, NAS, New York, New York, USA. September 18, 2002.
2002	Center for Biological Modeling, Michigan State University, East Lansing, Michigan, USA. September 27, 2002.
2002	Bioinformatics seminar, Texas A&M University, Tamu, TX, USA. November 7, 2002.
2002	Structure and Function of the Proteome, Argonne National Laboratory, Argonne, Illinois, USA. November 23-24, 2002.
2003	Keystone Symposium in Proteomics: Technologies and Applications, Keystone Resort in Keystone, Colorado, USA. March 25-30, 2003.
2003	NCRR sponsored Workshop on Structural Proteomics of Complexes, Bethesda, Maryland, USA. April 7-8, 2003.
2003	American Society for Biochemistry and Molecular Biology meeting, San Diego, California, USA. April 11-15, 2003.
2003	St. Jude Children's Research Hospital, Memphis, TN, USA. April 22, 2003.
2003	Genentech, Inc., South San Francisco, CA, USA. April 29, 2003.
2003	Structure and Function of Proteome, SBC, Argonne National Laboratory, Argonne, Illinois, USA. Spring, 2003.
2003	"Frontiers of Bioinformatics" symposium, Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York, USA. June 6-8, 2003.
2003	IBM Thomas J. Watson Research Center, New York, New York, USA. June 11, 2003.
2003	2003 Gordon Research Conference on 3D Electron Microscopy of Macromolecules, Colby Sawyer College, New London, New Hampshire, USA. June 22-26, 2003.
2003	PSI workshop ond data management, NIH Campus, Bethesda, MD, USA. July 10-11, 2003.
2003	GTL and Beyond: Data and Computational Needs Workshop, San Francisco, CA, USA. September 10-11, 2003.
2003	2003 Pharmaceutical Sciences and Pharmacogenomics Retreat, Marshall, CA, USA. September 11-13, 2003.
2003	Structure and Chemistry Seminar at Scripps, San Diego, CA, USA. September 18, 2003.
2003	Seminar at Northeastern University, Boston, MA, USA. October 6, 2003
2003	Workshop on Visualization of Biological Complexes, Four Points Sheraton Hotel, Emeryville, San Francisco Bay Bridge, CA, USA. October 11-12, 2003
2003	Seminar at PARC, Palo Alto, CA, USA. October 15, 2003.
2003	NIGMS Homology Modeling Workshop, Bethesda, MD, USA. October 21-22, 2003.
2003	Seminar at Purdue University, West Lafayette, IN, USA. October 24-25, 2003.
2003	PSI Target Selection Workshop, Bethesda, MD, USA. November 13-14, 2003.
2003	Biophysics/CCB Retreat, Asilomar Conference Center, Pacific Grove, CA, USA. December 7-9, 2003.
2004	Licensing Executives Society meeting, San Francisco, CA, USA. February 12, 2004
2004	The Structural, Functional and Evolutionary Gordon Conference, Four Points Sheraton Harbortown, Ventura, CA, USA. February 15-20, 2004.
2004	Seminar at Berkeley, Berkeley, CA, USA. March 8, 2004.
2004	Seminar at UCSC, Santa Cruz, CA, USA. March 11, 2004.
2004	Workshop on Structure Determination of Macromolecular Machines and Assemblies by Hybrid Methods, Granlibakken/Lake Tahoe Conference Center, CA, USA. March 17-20, 2004.
2004	Workshop on Structural Determination of Environmentally Responsive Gene (ERG) Products for Diagnostics & Drug Discovery (NIEHS/DERT), Snowbird Resort, Snowbird, Utah, USA April 12-13, 2004.
2004	2004 Keystone Symposium on Structural Genomics, Snowbird Resort, Snowbird, Utah, USA April 13-19, 2004.
2004	BayGenomics PGA, San Francisco, CA, USA. April 27, 2004.
2004	Gladstone Scientific Retreat, Asilomar in Monterey County, CA, USA. May 18-20. 2004.
2004	Seminar at Caltech, Pasadena, CA, USA. October 12, 2004.
2004	ICSG 2004 Meeting, Washington, DC, USA. November 17-24, 2004.
2004	Workshop of the Center of Protein Folding Machinery, Stanford University, CA, USA. December 4-5, 2004.
2004	Biological and Medical Informatics/Biophysics/Chemistry and Chemical Biology graduate groups retreat, Asilomar Conference Center, Pacific Grove, CA, USA. December 5-7, 2004.
2005	ABRF meeting, Biomolecular Technologies:Discovery to Hypothesis, Savanah, Georgia, USA. February 5-8, 2005.
2005	Frontiers in Computational Biophysics Symposium, NIH campus in Bethesda, MD, USA. April 29-30, 2005.
2005	NIH Symposium on Structural Analysis of Large Assemblies: Sizing up the Challenges, NIH campus in Bethesda, MD, USA. June 2-3, 2005.
2005	SRI’s Computational Biology series, SRI International, Menlo Park, CA, USA. June 29, 2005.
2005	19th Annual Symposium of the Protein Society, Boston, MA, USA. July 30 – August 3, 2005.
2005	GRC 2005 Computer-aided design meeting, Tilton School, NH, USA. July 31 – August 5, 2005.
2005	Seminar at the Biochemical and Biophysical Methods Course Fall 2005, The Rockefeller University, New York, NY, USA. October 11, 2005.
2005	Seminar at the Novartis Institutes for BioMedical Research, Cambridge, MA, USA. November 9, 2005.
2005	Workshop on Biological Macromolecular Structure Models, The State University of New Jersey, Piscataway, NJ, USA. November 19-20, 2005.
2006	Organizer and Speaker of the Theme “Macromolecular Structure and Dynamics” with 4 Symposia. ASBMB 2006 meeting, San Francisco, CA, USA. April 1-5, 2006.
2006	Seminar at UC Davis, CA. June 1, 2006.
2006	Symposium at Wyeth Research, Cambridge, MA, USA. October 16, 2006.
2006	Seminar at the University of Massachusetts, Dept. of Biochemistry and Molecular Pharmacology, Worcester, MA, USA. October 18, 2006.
2006	Seminar at the Fifth Annual Systems Biology Course at the Institute for Systems Biology, Seattle, WA, USA. 9 November 2006.
2006	Seminar at UC Merced Center for Computational Biology, Merced, CA, USA. 30 November 2006.
2006	TDR/WHO Drug Target Selection Meeting in Seattle, OR, USA. 1 December, 2006.
2006	Biological and Medical Informatics/Biophysics/Chemistry and Chemical Biology Graduate Groups Retreat, Monterey, CA, USA. 3-5 December, 2006.
2007	Collaborative Drug Discovery meeting, UCSF, San Francisco, USA. 1 March 2007
2007	The Protein Folding Center Annual Retreat, Stanford, CA, USA. 27-29 May 2007.
2007	Seminar at the Center for Theoretical Biological Physics. UCSD,San Diego USA. 1 June, 2007.
2007	Institute for Systems Biology, Seattle, WA, 12 July 2007.
2007	Seminar at Genentech, San Francisco, CA, 25 September 2007.
2007	Seminar at the SCRIPPS Institute, La Jolla, CA, USA. September 27-28
2007	Speaker and Organizer of the Modeling of Protein Interactions Meeting, MPI-2007, Lawrence, KA, USA, September 30 – October 2, 2007.
2007	Seminar at the Albert Einstein College of Medicine, New-York, NY. 16 October 2007.
2007	Seminar at University of California Berkeley, New-York, NY. 25 October 2007.
2007	Seminar at the Carolina Center for Genomic Sciences colloquium, UNC, Chapel Hill, NC, USA. 9 November 2007.
2007	Seminar at the Duke University Computational Biology Series, Durham, NC, USA. 12 November 2007.
2008	Keystone Symposium on Structural Genomics and Its Applications to Chemistry, Biology and Medicine, Steamboat Springs, Colorado, CO, USA, 6-11 January 2008.
2008	Seminar for the Biochemical and Biophysical Methods Course at the Rockefeller University, New York, NY. 30 January 2008
2008	Seminar at the University of Utah, February 25 2008.
2008	Seminar at The Buck Institute for Age Research, Novato, CA, USA, July 1 2008.
2008	Speaker and Organizer of the Protein Modeling Workshop, University of California, San Francisco, CA, USA, July 11-12 2008.
2008	Speaker at the 2008 Senior Vice Chancellor’s Laureate Lecture Series at the University of Pittsburgh, July 18 2008.
2008	Protein Structure Initiative (PSI3), Washington DC, USA, October 29-30, 2008.
2008	Seminar at UT Southwestern Medical Center, 5-6 Nov 2008.
2008	Biology and Mathematics in the Bay Area (BaMBA), University of California, Davis, CA,USA, November 15, 2008.
2008	Biological and Medical Informatics/Biophysics/Chemistry and Chemical Biology Graduate Groups Retreat, Monterey, CA, USA. 7-9 December, 2008.
2008	NCMI Single Particle Reconstruction Workshop, Baylor College of Medicine, Houston, TX, USA, December 10-13, 2008.
2009	Seminar at the University of Pennsylvania School of Medicine, Philadelphia, PA, USA, January 29, 2009.
2009	Mesilla Chemistry Workshop Multi-Scale Modeling of Biological Molecules, Mesilla, TX, USA, February 1-4, 2009.
2009	Technology Centers for Networks and Pathways Annual All Hands Meeting, Washington DC, USA, March 12-13, 2009
2009	2009 Symposium on Molecular Systems Biology of the Cell, Seattle, WA, USA, April 19, 2009.
2009	Seminar at the University of Minnesota, Minneapolis, MN, USA, April 22, 2009.
2009	Seminar at the University of Washington, Seattle, WA, USA, May 14, 2009.
2009	Seminar at Indiana University, Indianapolis, IN, USA, May 18, 2009.
2009	Seminar at University of Texas Southwestern, Dallas, TX, USA, May 20-21, 2009.
2009	23rd Annual Symposium of the Protein Society, Boston, MA, USA, July 25-29, 2009.
2009	Speaker at the Pharmaceutical Sciences and Pharmacogenomics Retreat, Tomales Bay, CA, USA, September 9-10, 2009.
2009	Beckman Institute 20th Anniversary Symposium, University of Illinois at Urbana-Champaign, Urbana, IL, USA, September 20-23, 2009.
2009	Seminar at University of Southern California, Los Angeles, CA, USA, November 19, 2009.
2009	Speaker at the Annual Computational and Theoretical Biology Symposium, Houston, TX, USA, December 4-6, 2009.
2010	Speaker and Co-Organizer of the Keystone Symposia on Structural Biology/Structural Genomics, Steamboat Springs, CO, USA, January 8-13, 2010.
2010	Speaker at the Modeling of Cryo-EM Map Workshop, Baylor College of Medicine, Houston, TX, USA, January 14-17, 2010.
2010	Chair and Speaker at the Biophysical Society 54th Annual Meeting, San Francisco, CA, USA, February 20-24, 2010.
2010	Speaker at the Hybrid Methods Symposium, Lake Tahoe, CA, USA, March 10-14, 2010.
2010	Speaker at the Structural Biology Symposium, Case Western Reserve University, Cleveland, OH, USA, May 19, 2010.
2010	Keynote Speaker at the 3Dsig Satellite Meeting, Boston, MA, USA, July 9-10, 2010.
2010	Speaker at the 18th International Conference on Intelligent Systems for Molecular Biology (ISMB 2010), Boston, MA, USA, July 11-13, 2010.
2010	Seminar at Vanderbilt University, Nashville, TN, USA, October 12, 2010.
2010	Seminar at Ohio State University, Columbus, OH, USA, October 26, 2010.
2010	Speaker at the MPI Meeting, University of Kansas, Lawrence, KS, USA, October 28-30, 2010.
2010	Seminar at the University of California, San Diego, CA, USA, December 12, 2010.
2011	Speaker at the Design of Drugs and Chemicals that Influence Biology Workshop, University of California, Los Angeles, CA, USA, April 4-8, 2011.
2011	Keynote Speaker at the Sanford-Burnham Structural Systems Biology Symposium, La Jolla, CA, USA, June 7, 2011.
2011	Speaker at the Institute for Systems Biology Symposium and Workshop, University of Washington, Seattle, WA, USA, July 24-27, 2011.
2011	Speaker at the Accelerating Predictive Drug Development Through Quantitative Pharmacology Symposium University of California, San Francisco, California, USA, September 22-23, 2011.
2011	Speaker at the Worldwide Protein Data Bank (wwPDB) Symposium, Cold Spring Harbor, NY, USA, October 28-30, 2011.
2011	Seminar at St. Jude Children’s Research Hospital, Memphis, TN, USA, November 15, 2011.
2011	Seminar at Duke University, Durham, NC, USA, November 18, 2011.
2012	Speaker and Co-organizer of the Keystone Symposia on High Throughput and Hybrid Approaches to Structural Biology, Keystone, CO, USA, January 22-27, 2012.
2012	Speaker at Eli Lilly Symposium, Indianapolis, IN, USA, February 13-14, 2012.
2012	Seminar at the University of Michigan, Ann Arbor, MI, USA, February 15, 2012.
2012	Seminar at the Scripps Research Institute, San Diego, CA, USA, March 1-2, 2012.
2012	Co-organizer of the 6th International Conference on Structural Analysis of Supramolecular Assemblies by Hybrid Methods, Lake Tahoe, CA, USA, March 14-18, 2012.
2012	Keynote Speaker at the ISMB, Long Beach, CA, USA, July 14-17, 2012.
2012	Speaker at the NRAMM Workshop, Scripps Research Institute, San Diego, CA, USA, November 16, 2012.
2013	Seminar at NIH, Bethesda, MD, USA, January 17, 2013.
2013	Speaker at the Herron Lecture, Florida State University, Tallahassee, FL, USA, February 15, 2013.
2013	Speaker at the Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA, March 28, 2013.
2014	Seminar at Harvard University, Cambridge, MA, USA, February 3, 2014
2014	Seminar at Columbia University, New York, NY, USA, February 5, 2014
2014	Seminar at the Scripps Research Institute, San Diego, CA, USA, February 24-25, 2014
2014	Seminar at UC Berkeley, Berkeley, CA, USA, March 10, 2014
2014	Keynote Speaker at the 2014 Biopolymers Gordon Research Conference, Newport, RI, USA, June 1-6, 2014
2014	Keynote Speaker at the 2014 Annual RosettaCon, Leavenworth, WA, USA, July 30 - August 1, 2014
2014	Speaker at the Peter Wright Symposium, University of California, San Francisco, CA, USA, September 15, 2014
2014	Speaker at the NCI Workshop at the Houston Methodist Research Institute at Texas Medical Center, Houston, TX, USA, September 18-19, 2014
2014	Organizer of the Martin Karplus Celebration Symposium, San Francisco, CA, USA, October 1, 2014
2014	Speaker at the International Society for the Study of Xenobiotics meeting, San Francisco, CA, USA, October 19-23, 2014
2014	Seminar at Rutgers University, New Brunswick, NJ, USA, October 29, 2014
2015	Seminar and Biophysics Course at the Scripps Research Institute, San Diego, CA, USA, February 26-27, 2015
2015	Speaker at the U.S. Human Proteome Organization (US-HUPO) Annual Meeting, Tempe, AZ, USA, March 15-18, 2015
2015	Speaker at the American Chemical Society National Meeting, Denver, CO, USA, March 22-26, 2015
2015	Seminar at the University of Florida, Gainesville, FL, USA, April 14, 2015
2015	Seminar at the Oregon Health and Science University, Portland, OR, USA, May 19, 2015
2015	Seminar at Department of Chemistry and Biochemistry, UCSD, San Diego, November 2-3, 2015.
2016	Speaker at the 2016 ASBMB Annual Meeting, San Diego, USA, April 6, 2016.
2016	Speaker at the 5th International Symposium on Higher Order Structure of Protein Therapeutics, Long Beach, USA, April 12, 2016.
2016	Organizer and Speaker at the Computational Biophysics Workshop, San Francisco Dec 12-16, 2016.
2017	Speaker at the QBI 2017 Cell Mapping Symposium, UCSF, San Francisco, CA, Sep 13-14, 2017.
2017	Seminar at the Rockefeller University, New York City, NY, Oct 24, 2017
2018	Speaker at the 2018 Keystone Symposia on Cryo-EM from Cells to Molecules: Multi-Scale Visualization of Biological Systems, Granlibakken, CA, Feb 4-9, 2018.
2019	Organizer of the 63rd Annual Meeting of the Biophysical Society, Baltimore, MD, Mar 2-6, 2019.
2019	Lecture in the Structural Biology Course at the Scripps Research Institute San Diego, CA, USA March 15-16, 2019.
2019	Speaker at Section 29 National Academy of Sciences Annual Meeting, DC, April 28, 2019.
2019	Lecturer in the Biochemical and Biophysical Methods I & II Course at the Rockefeller University, New York City, October 8, 2019.
2020	Lecture in the Structural Biology Course at the Scripps Research Institute San Diego, CA, USA, February 25 & 27, 2020.
2021	Seminar at the Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, October 28, 2021.
2023	Speaker at the 2023 ACS Fall Meeting, Kuntz symposium , San Francisco, CA, August 13-17, 2023.v
2023	Keynote speaker at the Peroxisome meeting, Seattle Childrens, Seattle, WA, September 10-12, 2023.
2023	Speaker at the 2ND Annual St. Jude Symposium on Structural and Computational Biology, St. Jude, Memphis, TN, October 2-3, 2023.
2023	Lecturer in the Biochemical and Biophysical Methods I & II Course at the Rockefeller University, New York City, October 10, 2023.
2024	Seminar at the Scripps Research Institute San Diego, CA, USA, February 15, 2024.
2024	Lecture in the Structural Biology Course at the Scripps Research Institute San Diego, CA, USA, February 17, 2024.
2024	Organizer and Speaker at the Bayesian Model Validation Workshop, RCSB, Interlaken Inn, Connecticut, January 17-18, 2024.
2024	Speaker at the Biophysical Society 68th Annual Meeting, Philadelphia, PA, February 10-14, 2024.
2024	Seminar at the Vanderbilt University, Nashville, TN, USA, March 24, 2024.
2024	2024 Faculty Research Lecture Award Basic Science at the University of California, San Francisco, San Francisco, CA, USA, April 16, 2024.

GOVERNMENT AND OTHER PROFESSIONAL SERVICE

2004 - 2009	National Institutes of Health	MSF-B Study Section (successor of BBCA)
1995 - present	NIH, National Science Foundation, DOE, European Community, Burroughs Welcome Fund, Binational Science Foundation	ad hoc Grant Reviews

UNIVERSITY AND PUBLIC SERVICE

SERVICE ACTIVITIES SUMMARY

I serve on a large number of committees at UCSF, including graduate program leadership, technical infrastructure, and faculty search committees.

UCSF CAMPUSWIDE

2003 - present	Ad hoc Faculty reviews (~40)
2003 - 2003	Future of Computing at UCSF Committee
2003 - 2007	MD/PhD Scientist in QB3 Search Committee
2003 - 2005	Byers Hall (QB3) Building Committee
2003 - 2005	Pharmaceutical Sciences and Pharmacogenomics Graduate Program Admissions Committee
2003 - present	Bioinformatics and Medical Informatics Graduate Program Executive Committee
2003 - 2004	Bioinformatics and Medical Informatics Graduate Program Admissions Committee
2003 - 2004	Biophysics Graduate Program Admissions Committee
2005 - present	iPQB Curriculum committee
2005 - present	iPQB Executive Committee
2005 - 2009	iPQB Admissions Committee
2004 - 2004	Chancellor's Council committee
2004 - 2004	Academic Information Technology Coordinator search committee
2004 - present	QB3@UCSF / QBI Executive Committee
2005 - 2008	Basic Sciences Research Resources Oversight Committee
2005 - 2011	Rock Hall Governance Committee
2005 - 2006	QB3 Governance/Community Committee, Chair
2005 - 2009	Mission Bay leadership committee
2006 - 2019	Faculty steering committee for the shared computer cluster at QB3, Chair
2003 - 2004	Bioinformatics and Computational Biology Faculty Search Committee, Co-Chair
2005 - 2010	Systems Biology Faculty Search Committee
2005 - 2008	Systems Biology HHMI/NIBIB Training Grant Leadership Committee
2007 - present	BMI Training Grant Leadership Committee
2007 - 2007	Quantitative Imaging Faculty Search Committee
2008 - 2008	Human Genetics Faculty Search Committee, Co-Chair
2011 - 2011	Pharmacometrics Faculty Search Committee
2011 - 2013	Bioinformatics Task Force
2011 - present	IT Governance Committee on Research Technology
2012 - 2015	Enabling Technologies Advisory Committee
2012 - 2012	Gladstone Institute Faculty Search Committee
2012 - 2015	ICHS Infrastructure Committee
2012 - 2013	Funding Shared Equipment Awards Committee
2012 - 2014	Bioimaging Faculty Search Committee
2013 - 2014	Data Center Services Advisory Board
2013 - 2014	2.0-Ideation for the Future of UCSF Committee
2013 - 2016	Shared Research Facilities Roadmap Steering Committee
2014 - 2016	Institute for Neurodegenerative Diseases Faculty Search Committee, Co-Chair
2015 - 2020	Chair, QB3 Shared Cluster Steering Committee
2016 - 2024	Basic Research - IT interactions committee
2016 - 2020	Executive Committee of Institute for Computational Health Sciences (ICHS)
2019 - 2024	Wynton faculty steering committee	Chair
2021 - 2024	IT Governance Committee on Research Technologies
2021 - 2024	Shared Cluster Computing Governance Committee

SCHOOL OF PHARMACY

2003 - 2008	SOP Information Technology Committee
2005 - 2005	SOP Strategic Planning Committee
2007 - 2007	SOP Advisory committee for sharing software royalties
2007 - 2007	SOP Advisory committee for developing the SOP price / performance metric
2007 - 2007	SOP Space allocation committee
2009 - present	SOP Outreach to industry program
2010 - 2011	SOP Faculty Awards Committee
2012 - 2014	SOP Educational Policy Committee
2014 - 2022	SOP Frontiers in Science and Practice of Therapeutics Committee
2015 - 2023	Associate Dean of Research
2015 - 2024	SOP leadership group

DEPARTMENTAL SERVICE

2003 - 2019	BTS Internal Advisory Committee
2013 - 2019	PSPG Graduate Program Admissions Committee

Contributions to UCSF PRIDE VALUES

Contributions to UCSF PRIDE Values

I have been involved in Public Service activities and indirectly even in Clinical activities for diverse patient populations. Perhaps the most significant such contribution is via my role as a co-founder and advisor of Global Blood Therapeutics Inc (NASDAQ GBT), aiming from the outset to develop a small molecule drug for the sickle cell disease, which in the US affects primarily African Americans; there is currently no effective drug for this debilitating and terminal disease. The company produced a drug candidate that is currently in accelerated Phase III clinical trials; GBT announced that FDA will pre-approve the drug as soon as GBT makes an appropriate request within the next few months. Based on all clinical evidence, the drug is efficacious and without significant side affects, and thus poised to significantly benefit hundreds of thousands of patients in the US and Europe, as well as eventually ~20 million patients in Africa. Another similar contribution was my scholarly work on open source drug discovery, with my colleagues Maurer and Rai, published in multiple papers listed in my publication list; this work was motivated by facilitating drug discovery for diseases that are not clearly commerically attractive to commercial drug discovery efforts, such as third world diseases.

TEACHING AND MENTORING

TEACHING SUMMARY

When I arrived to UCSF in January 2003, I joined Prof. Patsy Babbit in leading the graduate and professional students' courses in Bioinformatics (BMI-206 and BPS-114). In 2008-09, I took the primary responsibility for these two courses. I also gave many of the lectures and supervised student activity associated with the courses (eg, student seminars, exercise sets). Since 2010, I contribute several lectures to BMI-206, but the course is led by others (BPS-114 does not exist anymore). I also participate as a guest lecturer in a number of other courses, such as Macromolecules and Chem 204. Between 2014 and 2019, I contributed a number of lectures in BPS-134, a course for pharmacy students, led by Nancy Sambol. Finally, I am involved in the shaping of the curriculum for the graduate programs in the iPQB umbrella program, as a member of the BMI executive committee and a contributor to the training grant re-submissions.

FORMAL TEACHING

Academic Yr	Course No. & Title	Teaching Contribution	School	Class Size
2004 - 2004	Bioinformatics BMI-206	Co-Organizer, Lecturer		15
2005 - 2005	Bioinformatics BMI-206	Co-Organizer, Lecturer		15
2005 - 2005	Bioinformatics BPS-114	Co-Organizer, Lecturer		130
2006 - 2006	Bioinformatics BMI-206	Co-Organizer, Lecturer		15
2006 - 2006	Bioinformatics BPS-114	Co-Organizer, Lecturer		130
2007 - 2007	Bioinformatics BMI-206	Co-Organizer, Lecturer		15
2007 - 2007	Bioinformatics BPS-114	Co-Organizer, Lecturer		130
2007 - 2007	Bioinformatics BMI-206	Co-Organizer, Lecturer		15
2007 - 2007	Bioinformatics BPS-114	Co-Organizer, Lecturer		130
2008 - 2008	Bioinformatics BMI-206	Organizer, Lecturer		15
2008 - 2008	Bioinformatics BPS-114	Organizer, Lecturer		130
2009 - 2009	Bioinformatics BMI-206	Organizer, Lecturer		15
2009 - 2009	Bioinformatics BPS-114	Lecturer		130
2010 - 2010	Bioinformatics BMI-206	Organizer, Lecturer		15
2012 - 2012	Bioinformatics BMI-206	Lecturer		15
2013 - 2013	Bioinformatics BMI-206	Lecturer		15
2013 - 2013	BPS 134	Lecturer		6
2013 - 2013	NSF Proposal Course	Lecturer
2014 - 2014	NSF Proposal Course	Lecturer
2014 - 2014	Bioinformatics BMI-206	Lecturer		15
2014 - 2014	BPS 134	Lecturer		6
2003 - present	Macromolecular Interactions BP-204	Occasional Guest Lecturer		20
2011 - present	Chem 204	Guest Lecturer		3
2015 - present	Systems Pharmacology, Pharmacogenomics 245B	Guest Lecturer		15
2015 - 2015	BPS 134	Lecturer		6
2016 - 2016	BPS 134	Lecturer		10
2017 - 2017	BPS 134	Lecturer		10
2018 - 2018	BPS 134	Lecturer		10
2018 - 2020	BMI 203	Organizer, Lecturer		15

MENTORING SUMMARY

I have been involved in both formal and informal teaching at UCSF, as illustrated by my contributions to the graduate courses, professional courses, and mentoring of students and postdocs in my laboratory, detailed in the corresponding sections of this cv.

PREDOCTORAL STUDENTS SUPERVISED OR MENTORED

Dates	Name	Program or School	Mentor Type	Role	Current Position
1995 - 2000	Roberto Sanchez	Rockefeller University		PhD Advisor	Associate Professor, Mount Sinai School of Medicine, NY
1999 - 2001	Eric Feyfant	Rockefeller University		PhD Advisor	Senior Scientist, Wyeth Inc. Cambridge, MA.
1999 - 2003	Nebojsa Mirkovic	Rockefeller University		PhD Advisor	Postdoctoral fellow with Diana Murray at Weill Medical College of Cornell University, NY
2000 - 2003	Bino John	Rockefeller University		PhD Advisor	Assistant Professor, University of Pittsburg
2002 - 2008	Ranyee Chiang	BMI		PhD Advisor	Postdoc at New York University
2003 - 2007	Fred Davis	Biophysics		PhD Advisor	Postdoc at Janelia Farm, HHMI
2003 - 2008	Michael Kim	BMI		PhD Advisor	The Mechanical Zoo
2003 - 2008	Libusha Kelly	BMI		PhD Advisor	Postdoc at MIT, with Penny Chisholm
2004 - 2008	David Eramian	Biophysics		PhD Advisor	Patent Counsel, eBay Inc.
2005 - 2008	Mark Peterson	BMI		PhD Advisor	The Boston Consulting Group
2006 - 2011	David Barkan	BMI		PhD Advisor	Staff Scientist, Protaganist Therapeutics
2006 - 2011	Keren Lasker	Tel-Aviv University		PhD Advisor	Postdoctoral Fellow, Stanford UniversityWolfson
2007 - 2009	Adam Marko	BMI		MSc Advisor	Asuragen, Inc., Austin, TX Bioinformatics Developer
2007 - 2012	Jeremy Phillips	BMI		PhD Advisor	Bioinformatics Analyst, Genome Institute/LBL
2009 - 2014	Peter Cimermancic	BMI		PhD Advisor	UCSF Specialist
2011 - 2015	Natalia Khuri	Biophysics		PhD Advisor	Educational Program Director, UCSF-Stanford CERSI Lecturer,
2010 - 2016	Charles Greenberg	BMI		PhD Advisor	Data Scientist @ APPLE
2012 - 2016	Adrian Stecula	PSPG		PhD Advisor	Atomwise
2012 - 2016	Sara Calhoun	Biophysics		PhD Advisor	Data Scientist @ Joint Genome Institute
2014 - 2021	Ilan Chemmama	Biophysics		PhD Advisor	BrightSeed
2015 - 2021	Seth Axen	Biophysics		PhD Advisor	Machine Learning Engineer @ University of Tubingen
2018 - 2022	Laurel Estes	BMI	Research/Scholarly Mentor	Academic Advisor	Graduate Student
2018 - 2022	Wren Saylor	BMI	Research/Scholarly Mentor	Academic Advisor	Graduate Student
2018 - 2022	Stephanie Wankowicz	BMI	Research/Scholarly Mentor	Academic Advisor	Graduate Student
2018 - 2022	Cole Helsell	iPQB	Research/Scholarly Mentor	Academic Advisor	Graduate Student
2018 - 2019	Bryan Faust	Biophysical	Research/Scholarly Mentor	Academic Advisor	Graduate Student
2018 - 2019	Nick Hoppe	Biophysical	Research/Scholarly Mentor	Academic Advisor	Graduate Student
2021 - 2024	Matthew Hancock	Biophysical	Research/Scholarly Mentor	Academic Advisor	Graduate Student
2021 - 2024	Aji Palar	Biophysical	Research/Scholarly Mentor	Academic Advisor	Graduate Student
2024 - present	Catherine Sue	PSPG	Research/Scholarly Mentor	Academic Advisor	Graduate Student
2024 - present	Mark Ware		Research/Scholarly Mentor	Academic Advisor	Graduate Student

POSTDOCTORAL FELLOWS AND RESIDENTS MENTORED

Dates	Name	Fellow	Mentor Role	Faculty Role	Current Position
1995 - 1997	Ilya Vakser	Postdoc Scholar		Research supervision	Professor, University of Kansas, Lawrence, KS
1996 - 1999	Azat Badretdinov	Postdoc Scholar		Research supervision	Senior scientific programmer at Accelrys Inc., San Diego
1997 - 2002	Andras Fiser	Postdoc Scholar		Research supervision	Associate Professor, Albert Einstein College of Medicine, Bronx, NY
1998 - 2001	Francisco Melo	Postdoc Scholar		Research supervision	Associate Professor, Pontificia Universidad Catolica de Chile
1999 - 2003	Ash Stuart	Postdoc Scholar		Research supervision	Assistant Professor, Ramapo College, Mahwah, NJ
1999 - 2006	Marc Marti-Renom	Adjunct Assistant Professor		Research supervision	Assistant Professor, Prince Felipe Research Center, Valencia, Spain
2000 - 2002	Valya Ilyin	Scientific Programmer		Research supervision	Associate Professor, Northeastern University, Boston
2000 - 2006	Andrea Rossi	Postdoc Scholar		Research supervision	Senior Scientist, Rinat Laboratories, Pfizer Inc.
2000 - 2007	M.S. Madhusudhan	Postdoc Scholar		Research supervision	Assistant Professor, Bioinformatics Insitute, Singapore
2000 - 2008	Narayanan Eswar	Scientific Programmer		Research supervision	Group Leader, Du Pont Inc.
2000 - 2014	Ursula Pieper	Scientific Programmer		Research supervision	Web Applications Specialist, National Agricultural Library
2001 - 2007	Frank Alber	Postdoc Scholar		Research supervision	Assistant Professor, University of Southern California
2002 - 2003	Bozidar Yerkovich	Scientific Programmer		Research supervision	Head of Structural Bioinformatics at Rosetta Inpharmatics Inc., Seattle
2002 - 2006	Damien Devos	Postdoc Scholar		Research supervision	Senior postdoc with Rob Russell, EMBL, Heidelberg
2002 - 2007	Dmitry Korkin	Postdoc Scholar		Research supervision	Assistant Professor, University of Missouri at Columbia
2003 - 2004	Niu Huang	Postdoc Scholar		Research supervision	Assistant Professor, Beijing, China
2003 - 2006	Maya Topf	Postdoc Scholar		Research supervision	Lecturer, Department of Crystallography, Birkbeck College, London
2003 - 2006	Rachel Karchin	Postdoc Scholar		Research supervision	Assistant Professor, Johns Hopkins University
2003 - 2008	Min-yi Shen	Postdoc Scholar		Research supervision	Postdoc researcher
2003 - present	Ben Webb	Scientific Programmer		Research supervision	Scientific Programmer
2005 - 2008	Friedrich Foerster	Postdoc Scholar		Research supervision	Postdoc researcher
2006 - 2013	Javier Velazquez	Postdoc Scholar		Research supervision	Cypher Genomics Bioinformatics Analyst
2006 - 2014	Hao Fan	Postdoc Scholar		Research supervision	A*STAR, Singapore Principal Investigator
2007 - 2014	Daniel Russel	Postdoc Scholar		Research supervision	AltSchool Senior Research Engineer
2008 - 2012	Avner Schlessinger	Postdoc Scholar		Research supervision	Mount Sinai School of Medicine Assistant Professor
2008 - 2015	Dina Schneidman	Postdoc Scholar		Research supervision	Specialist
2008 - 2018	Seung-Joong Kim	Postdoc Scholar		Research supervision	KAIST, Daejeon, Korea
2009 - 2011	Sebnem Essiz	Postdoc Scholar		Research supervision	Assistant Professor, Kadir Has University, Istanbul
2009 - 2014	Guangqiang Dong	Postdoc Scholar		Research supervision	Data Scientist, Facebook
2009 - 2014	Patrick Weinkam	Postdoc Scholar		Research supervision	Lead Engineer, Data Science, Baselayer
2009 - 2015	Elina Tjioe	Postdoc Scholar		Research supervision	Scientific Programmer
2010 - 2011	Backy Chen	Postdoc Scholar		Research Supervision	Institute of Biomedical Science, Academia Sinica, Taiwan, Postdoc Researcher
2010 - 2013	Massimiliano Bonomi	Postdoc Scholar		Research Supervision	Institut Pasteur, Group lead
2010 - 2013	Riccardo Pellarin	Postdoc Scholar		Research Supervision	Postdoctoral Fellow, Institut Pasteur
2011 - 2012	Lan Hua	Postdoc Scholar		Research Supervision	Postdoc researcher
2012 - 2013	Miriam Sgobba	Postdoc Scholar		Research Supervision	Postdoc researcher
2012 - 2020	Barak Raveh	Postdoc Scholar		Research Supervision	Hebrew University, PI
2014 - 2016	Peter Cimermancic	Postdoc Scholar		Research Supervision	Pathology Machine Learning Team Lead at Verily Life Sciences
2014 - present	Shruthi Viswanath	Postdoc Scholar		Research Supervision	NCBS, PI
2014 - 2017	Kate Stafford	Postdoc Scholar		Research Supervision	Senior Scientist - Atomwise
2014 - 2020	Daniel Saltzberg	Postdoc Scholar		Research Supervision	Postdoc researcher
2015 - present	Ignacia Echeverria	Postdoc Scholar		Research Supervision	Assistant Professor, Cellular Molecular Pharmacology, UCSF
2016 - 2021	Sai Ganesan	Postdoc Scholar		Research Supervisor	Software Engineer, Machine Learning Google
2016 - 2019	Nikita Chopra	Postdoc Scholar		Research Supervisor	Senior Scientist I Schrödinger
2017 - 2020	Kala Pilla	Postdoc Scholar		Research Supervisor	Computational Structural Biologist Etcembly Ltd
2017 - 2022	Jeremy Tempkin	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor,Career Mentor	Research Supervisor	Scientist, LLNL
2017 - 2023	Rakesh Ramachandran	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor,Career Mentor	Research Supervisor	Postdoc researcher
2018 - 2020	Leah Ray	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor,Career Mentor	Research Supervisor	Manager, Medical Writing at Pfizer
2018 - 2022	Thomas-Otavio Peulen	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor,Career Mentor	Research Supervisor	Postdoctoral Scientist Rudolf Virchow Centre for Integrative and Translational Bioimaging
2019 - 2022	Tanmoy Sanyal	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor,Career Mentor	Research Supervisor	Scientist, Computational drug discovery Novo Nordisk
2020 - 2022	Dibyendu Mondal	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor,Career Mentor	Research Supervisor	Scientist Biogen
2021 - present	Neelesh Soni	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor,Career Mentor	Research Supervisor	Postdoc researcher
2022 - present	Andrew Latham	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor,Career Mentor	Research Supervisor	Postdoc researcher
2022 - present	Arthur Zalevsky	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor,Career Mentor	Research Supervisor	Postdoc researcher
2023 - present	Abantika Pal	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor,Career Mentor	Research Supervisor	Postdoc research
2023 - present	Kenneth Huang	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor,Career Mentor	Research Supervisor	Postdoc research
2023 - present	Eli Draizen	Postdoc Scholar		Research Supervisor	Postdoc research
2023 - present	Surabhi Rathore	Postdoc Scholar		Research Supervisor	Postdoc research
2022 - 2024	Tracy Wang	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor	Research Supervisor	Postdoc research
2023 - present	Atreya Dey	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor	Research Supervisor	Postdoc researcher
2023 - 2024	Eliot Jefferys	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor	Research Supervisor	Postdoc researcher
2023 - present	Vipul Kumar	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor	Research Supervisor	Postdoc researcher
2023 - present	Jared Sagendorf	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor	Research Supervisor	Postdoc researcher
2023 - present	Vikas Tiwari	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor	Research Supervisor	Postdoc researcher
2024 - present	Sree Ganesh Balasubramani	Postdoc Scholar	Research/Scholarly Mentor,Project Mentor	Research Supervisor	Postdoc researcher

FACULTY MENTORING

Dates	Name	Position while Mentored	Mentor Type	Mentoring Role	Current Position
2015 - present	Ignacia Echeverria	Postdoc		Mendor	Associate Professor, BTS
2013 - present	Sourav Bandyopadhyay	Assistant Professor		Mentor	Assistant Professor, BTS
2012 - present	Graham Johnson	Fellow		Mentor	QB3 Fellow, BTS
2010 - present	Ryan Hernandez	Assistant Professor		Mentor	Assistant Professor, BTS
2011 - present	Rada Savic	Assistant Professor		Mentor	Assistant Professor, BTS
2004 - 2013	Tanja Kortemme	Assistant Professor		Mentor	Professor, BTS
2007 - 2008	Mats Gustafsson	Assistant Professor		Mentor	Assistant Professor, Physiology

RESEARCH AND CREATIVE ACTIVITIES

RESEARCH AND CREATIVE ACTIVITIES SUMMARY

I have a broad background in computational structural biology, with the emphasis on structural modeling and simulations: I have developed and applied methods for comparative protein structure modeling, functional annotation of proteins, and integrative structure determination of macromolecular assemblies, as well as contributed to the understanding of the protein folding process. For example, in the field of protein structure prediction, I introduced homology or comparative modeling by satisfaction of spatial restraints, which utilizes both physical and statistical information, thereby improving its accuracy and applicability. The corresponding program, MODELLER, has been licensed to over 50,000 academic users, as well as many pharmaceutical groups, and is perhaps the most widely used program for comparative modeling. The resulting database of models for approximately 6 million known protein sequences, ModBase, is linked bi-directionally to a number of key biological databases, including UniProt. My major current research objective is to develop and apply a computational system for enumerating structures of protein assemblies that are consistent with all available information from experimental methods, physical theories, and statistical inference. Such an integrative system will maximize efficiency, accuracy, resolution, and completeness of the structural coverage of macromolecular assemblies. The current version of the corresponding program, Integrative Modeling Platform (IMP), is being used to determine the structures of a number of macromolecular assemblies, in collaboration with experimentalists. Most prominently, the approach already enabled the determination of the configuration of the 456 proteins in the yeast Nuclear Pore Complex and 19 proteins in the 19S subunit of the 26S proteasome.

1. Integrative structural biology. Samples of many biological macromolecules prove recalcitrant to mainstream structural biology methods. In such cases, structures can often be determined by consideration of complementary information from multiple methods. Thus, we are developing mathematical formalism and open source computer software for enumerating structures of macromolecular assemblies that are consistent with all available information from experimental methods, physical theories, and statistical preferences extracted from biological databases (IMP; http://integrativemodeling.org). To achieve this objective, we formulated the problem as an optimization task, requiring a hierarchical representation of the modeled system, a scoring function that incorporates input information, and a sampling scheme that finds good scoring solutions. The integrative approach facilitates maximizing the accuracy, precision, completeness, and efficiency of the structural coverage of biomolecular systems. In addition, we are contributing to the nucleation of the scientific community concerned with computation, validation, visualization, archival, and dissemination of integrative structures, in part through several advisory groups associated with the Protein Data Bank, Keystone Symposia SAB, and editing of Structure.

F. Alber, S. Dokudovskaya, L. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni, R. Williams, B.T. Chait, M.P Rout, A. Sali. “Determining the architectures of macromolecular assemblies.” Nature 450, 683-694, 2007. PMID: 18046405

F. Alber, F. Förster, D. Korkin, M. Topf, A. Sali. “Integrating Diverse Data for Structure Determination of Macromolecular Assemblies.” Ann Rev Biochem 77, 443-477, 2008. PMID: 18318657

F. Forster, B. Webb, K.A. Krukenberg, H. Tsuruta, D.A. Agard, A. Sali. "Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies." J Mol Biol 382, 1089-1106, 2008. PMCID: PMC2745287

Russel D, Lasker K, Webb B, Velazquez-Muriel J, Tjioe E, Schneidman-Duhovny D, Peterson B, Sali A. Putting the pieces together: integrative structure determination of macromolecular assemblies. PLoS Biol 10, e1001244, 2012. PMCID: PMC3260315

2. Determining structures of macromolecular assemblies. It is essential for developers of computational methods to collaborate with experimentalists in applying their methods to practical problems. Such applications provide a validation of the methods as well as feedback for further development. Since 2001, we applied our integrative structure determination approach to over 20 macromolecular assemblies, exemplified by the four papers listed below. The resulting structures often facilitated insights into their evolution, function, and modulation.

C.M. Spahn, R. Beckmann, N. Eswar, P.A. Penczek, A. Sali, G. Blobel, J. Frank. "Structure of the 80S ribosome from Saccharomyces cerevisiae tRNA-ribosome and subunit-subunit interactions." Cell 107, 373-386, 2001. PMID: 11701127

F. Alber, S. Dokudovskaya, L. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni, R. Williams, B.T. Chait, A. Sali, M.P. Rout. “The Molecular Architecture of the Nuclear Pore Complex.” Nature 450, 695-701, 2007. PMID: 18046406

Lasker K, Forster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W. Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci USA 109, 1380-1387, 2012. PMCID: PMC3277140

J. Erzberger, F. Stengel, R. Pellarin, S. Zhang, T. Schaefer, C. Aylett, P. Cimermancic, D. Boehringer, A. Sali, R. Aebersold, N. Ban. "Molecular architecture of the 40S•eIF1•eIF3 translation initiation complex." Cell 158, 1125-1135, 2014. PMCID: PMC4151992

3. Development of comparative protein structure modeling. The accuracy of homology or comparative modeling is limited by the information that can be used in model calculations. Thus, we introduced comparative modeling by satisfaction of spatial restraints, which utilizes both physical and statistical information, thereby improving its accuracy and applicability. The corresponding program, MODELLER, has been distributed to over 50,000 academic users as well as many pharmaceutical groups, and is perhaps the most widely used program for comparative modeling. Because the genomic scale of biological data sets and accessibility require automation, we improved and implemented the entire process of comparative modeling, including fold assignment, sequence-structure alignment, model building, and model assessment, allowing us to calculate useful models for domains in ~65% of all known protein sequences. The resulting database, ModBase, is linked bi-directionally to UniProt at EBI and several other major biological databases. Our comparative modeling results led us to suggest some key aspects of the target selection strategies for the structural genomics initiative.

A. Sali, T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234, 779-815, 1993. PMID: 8254673

A. Fiser, R.K.G. Do, A. Sali. "Modeling of loops in protein structures." Protein Sci 9, 1753-1773, 2000. PMID: 11045621

B. John, A. Sali. "Comparative protein structure modeling by iterative alignment, model building and model assessment." Nucleic Acids Res 31, 3982-3992, 2003. PMID: 12853614

M.-Y. Shen, A. Sali. “Statistical Potential for Assessment and Prediction of Protein Structure” Protein Science 15, 2507-2524, 2006. PMID: 17075131

4. Development of methods for annotation of protein function. We have contributed a number of concepts, methods, programs, web servers, and databases in the bioinformatics toolbox for structure-based functional annotation of proteins (http://salilab.org). Examples include a machine-learning method for predicting functional consequences of single point mutations in proteins, optimized protocols for virtual screening against comparative models, various methods for predicting functional sites and localizing cryptic sites on protein structures, as well as databases of protein-protein interfaces and protein-small molecule interactions. To maximize our impact, we are also applying these tools in collaboration with biologists. An example is our extensive characterization of ABC and SLC membrane transporters, including mapping their evolution by classification, identification of their ligands by virtual screening and experimental validation, and prediction of functional impact of their point mutants; these studies contributed to structural genomics of ABC and SLC transporters.

R. Karchin, M. Diekhans, L. Kelly, D.J. Thomas, U. Pieper, N. Eswar, D. Haussler, A. Sali. "LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources." Bioinformatics 21, 2814-2820, 2005. PMID: 15827081

F.P. Davis, A. Sali. "PIBASE: a comprehensive database of structurally defined protein interfaces." Bioinformatics 21, 1901-1907, 2005. PMID: 15657096

A. Schlessinger, E. Geier, H. Fan, J. Irwin, B. Shoichet, K. Giacomini, A. Sali. "Structure-based Discovery of Prescription Drugs that Interact with the Norepinephrine Transporter, NET." Proc Natl Acad Sci USA 108, 15810-15815, 2011. PMID: 21885739

U. Pieper, B. Webb, G.Q. Dong, D. Schneidman-Duhovny, H. Fan, S.J. Kim, N. Khuri, Y. Spill, P. Weinkam, M. Hammel, J. Tainer, M. Nilges, A. Sali. "ModBase, a database of annotated comparative protein structure models, and associated resources." Nucleic Acids Res 42, 336-346, 2014. PMCID: PMC3965011

5. Insights into protein folding and allostery. We used a simple 3D lattice model of a protein chain to contribute to the current view of protein folding, which suggests that proteins can often fold via an ensemble of pathways, not a single one. Simulations suggested that the necessary and sufficient condition for a sequence to fold rapidly was a pronounced energy minimum for the native state. This finding was explained by an elementary, three-stage random search mechanism of folding. The rate-limiting step was a random search by local chain rearrangement in the semi-compact part of the phase space; a resolution of the Levinthal paradox without recourse to a folding pathway was made possible by a sufficiently small ratio between the numbers of states in the semi-compact and transition regions. The pronounced energy minimum of a folding sequence allowed the search to take place at a temperature that was high enough for the chain to rearrange efficiently, but also low enough for the native state to remain thermodynamically stable. More recently, we used realistic multi-minima Gõ models to simulate allostery at atomic resolution, and predict impact of point mutations on the allostery mechanism.

A. Sali, E. Shakhnovich, M. Karplus. "How does a protein fold?" Nature 369, 248-251, 1994. PMID: 7710478

A. Sali, E. Shakhnovich, M. Karplus. "Kinetics of protein folding. A lattice model study of the requirements for folding to the native state." J Mol Biol 235, 1614-1636, 1994. PMID: 8107095

P. Weinkam, J. Pons, A. Sali. "Structure-based Model of Allostery Predicts Coupling Between Distant Sites." Proc Natl Acad Sci USA 109, 4875-4880, 2012. PMCID: PMC3324024

P. Weinkam, Y.C. Chen, J. Pons, A. Sali. "Impact of mutations on the allosteric conformational equilibrium." J Mol Biol 425, 647-661, 2013. PMCID: PMC3557769

RESEARCH AWARDS - CURRENT

1.	OT2OD032742	PI	1 % effort	Sali (PI)
	OD		09/01/2022	08/30/2026
	Building an Interpretable Genomic Translator Using Maps of Cell Architecture		$ 978,891 direct/yr 1	$ 4,894,457 total
	To perform integrative structure modeling of the multi-protein systems of interest to the CM4AI center
2.	2022-252583	PI	2 % effort	Sali (PI)
	Silicon Valley Community Foundation		11/01/2022	10/31/2024
	Integrating the Software Toolkit for Protein Structure Modeling (EOSS-5)		$ 162,500 direct/yr 1	$ 325,000 total
	Our major goal is to create an interface between our IMP program for integrativestructure modeling and the PHENIX program for molecular modeling based on Xraycrystallography data.
3.	DBI - 1832184	Co - Investigator	1% % effort	Burley (PI)
	NSF/ Rutgers Univ		01/01/2019	12/31/2028
	PDB Management by the Research Collaboratory for Structural Bioinformatics		$ 220,000 direct/yr 1	$ 881,853 total
	The goal is to implement and test validation methods for integrative structures in the OneDep pipeline of wwPDB.
4.	P41 GM109824	Co-Investigator	10 % effort	Rout (PI)
	NIH		05/01/2019	04/30/2025
	National Center for Dynamic Interactome Research		$ 189,269 direct/yr 1	$ 1,225,149 total
	The central goal of the proposed National Center for Dynamic Interactome Research (NCDIR) is to address the urgent need for technologies that can rapidly, reliably and routinely reveal and interpret the dynamic cellular interactome.
5.	R01GM112108	Co-Investigator	3% % effort	Rout (PI)
	NIH		05/01/2019	04/01/2024
	Structure-Function Mapping of the Nuclear Pore Complex			$ 219,512 total
	The goal is to construct a model of the transport through the Nuclear Pore Complex, based on varied theoretical considerations and experimental datasets.
6.	P01AG002132	Co-Investigator	5 % effort	Prusiner (PI)
	NIH		6/16/2020	03/31/2025
	Degenerative and Dementing Diseases of Aging		$ 140,000 direct/yr 1	$ 1,533,776 total
	The central goal is mapping protein self-assemblies that lead to a number of neurodegenerative and systemic disorders.
7.	R01 GM083960	PI	10 % effort	Sali (PI)
	NIH/NIGMS		09/01/2021	08/31/2025
	IMP: Software for Hybrid Determination of Macromolecular Assembly Structures		$ 220,000 direct/yr 1	$ 1,975,036 total
	The goal is to develop and implement methods for integrative modeling of macromolecular assembly structures in the open source IMP package and to support its distribution.
8.	U54CA274502	Co-Investigator	10 % effort	Krogan (PI)
	NCI		09/01/2022	08/31/2027
	The Cancer Cell Map Initiative v2.0		$ 505,528 direct/yr 1	$ 2,527,644 total
	To compute integrative structural models of the target cancer- associated protein complexes, based on varied experimental data.
9.	U19AI171110	PI - Core 4	25 % effort	Sali (PI)
	NIAID		05/01/2022	04/30/2025
	QCRG Pandemic Response Program		$ 1,076,666 direct/yr 1	$ 3,230,000 total
	The major goals of this program are to develop specific inhibitors against select viral targets to advance to drug candidacy with our pharmaceutical partners. The AI Core will compute integrative structural models of the target viral systems, based on varied experimental data.
10.	U54AI170792	Co-Investigator	5 % effort	Krogan (PI)
	NIAID		07/01/2022	06/30/2027
	HARC: HIV accessory and regulatory complexes		$ 898,460 direct/yr 1	$ 28,625,946 total
	The HARC Center’s powerful “Systems-to-Structure” platform will uncover the mechanisms that allow HIV to inhibit host restriction factors, reveal the factors regulating HIV transcription and latency, and investigate virus host evolution to identify new treatment strategies by targeting key cellular processes.
11.	U19AI135990	Co-Investigator	1 % effort	Krogan (PI)
	NIAID		08/01/2018	07/31/2028
	HPMI: Host Pathogen Map Initiative			$ 807,210 total
	The goal is to apply integrative structure modeling to host-pathogen complexes identified by the consortium.

RESEARCH AWARDS - PAST

1.	R01 GM54762	PI
	NIH/NIGMS		07/01/1996	06/30/2010
	Protein Modeling by Satisfaction of Spatial Restraints		$ 200,000 direct/yr 1	$ 2,500,000 total
2.	U54 GM103511	Co-PI
	NIH/NIGMS		06/10/2005	07/31/2014
	Nucliear Information Pathway Center		$ 273,439 direct/yr 1	$ 2,100,000 total
3.	P01 GM71790	Collaborator
	NIH/NIGMS		07/01/2004	06/30/2014
	Deciphering Enzyme Specificity		$ 96,350 direct/yr 1	$ 800,000 total
4.	Sinsheimer Scholar Award	PI
	Alexandrine and Alexander L. Sinsheimer Fund		09/01/1996	08/31/1998
	Knowledge-Based Protein Structure Modeling for Genome Projects
5.	BIR-9601845	PI
	NSF		10/01/1996	09/30/1998
	Acquisition of a Multiprocessor Computer for Computational Physics and Structural Biology
6.	Gift	PI
	Molecular Simulations, Inc.		07/01/1998	07/01/1998
7.	Alfred P. Sloan Fellowship	PI
	Alfred P. Sloan Foundation		10/01/1998	9/30/2000
8.	R01 HL63284	Collaborator
	NIH/NHLBI		09/01/1999	08/31/2003
	Disruption and Expression of Mast Cell Protease Genes
9.	Mathers Foundation Award	PI
	Mathers Foundation		01/01/2000	12/31/2002
	Comparative Annotation of Eukaryotic Genomes: From Gene Detection to Protein Structure Modeling
10.	Career Scientist Award	PI
	Irma T. Hirschl Monique Weill-Caulier Trust		01/01/2000	12/31/2004
	Comparative Protein Structure Modeling for Genomics
11.	The Merck Genome Research Institute Award	PI
	The Merck Genome Research Institute		02/01/2000	01/31/2002
	Database of Comparative Protein Structure Model for Genomics
12.	R33 CA84699	Co-PI
	NIH/NCI		02/01/2000	01/31/2003
	Target Selection for the Structural Genomics of Cancer
13.	Gift	PI
	Prospect Genomics, Inc.		07/01/2000	07/01/2000
14.	U54 GM074945	Co-PI
	SGX/NIH		09/30/2000	08/31/2010
	NYSGRC: A Large-Scale Center for the Protein Structure Initiative		$ 261,032 direct/yr 1	$ 2,700,000 total
15.	R33 C89810	Collaborator
	NIH/NCI		06/01/2001	03/31/2004
	Comprehensive Map of Cellular Protein Interactions
16.	EDUD-7824-020257-US	PI
	Sun Academic Equipment Grant		07/03/2001	07/03/2001
	Development of an Integrated Software Environment for High-Throughput Structural Biology and Automated Comparative Protein Structure Modeling
17.	RGP67/2003	Co-PI
	Human Frontier Science Program Organization		07/01/2003	06/30/2006
	3-D Reconstruction and Identification of Postsynaptic Molecular Complexes Images by Electron Cryotomography
18.	Sandler Center for Basic Research in Parasitic Diseases	Collaborator
	Sandler Family Supporting Foundation		07/01/2003	06/30/2010
	Bioinformatics of Host-Pathogen Interactions
19.	California Institute for Quantitative Biomedical Research	PI
			08/01/2003	07/31/2005
	Towards a Comprehensive Map of Protein-Ligand Interactions
20.	SUR Equipment Award	PI
	IBM, Inc.		08/03/2003	08/03/2003
	Large-Scale Protein Structure Modeling and Ligand Docking
21.	Equipment Award	PI
	Intel, Inc.		09/15/2003	09/15/2003
	Large-Scale Protein Structure Modeling and Ligand Docking
22.	EIA-0324645	Co-PI
	NSF		11/01/2003	10/31/2006
	Subnanometer Structure-Based Fold Determination of Biological Complexes
23.	Opportunity Award	PI
	Sandler Program in Basics Sciences		02/15/2004	02/14/2006
	Hierarchical Framework for Structural Biology
24.	P01 AI035797	Core PI
	NIH/AI		07/01/2004	06/30/2009
	Targeting Cysteine Proteases - Antiparasitic Chemotherapy
25.	IIS-0705196	PI
	NSF		08/01/2007	07/31/2009
	Integrated Modeling of Biological Nanomachines
26.	EF 0626651	Collaborator
	NSF		01/01/2008	10/31/2010
	The PhyloFacts Phylogenomic Encyclopedia of Microbial Protein Families		$ 17,261 direct/yr 1	$ 35,387 total
27.	Pfizer / QB3 Award	PI
	Pfizer, Inc.		09/01/2008	08/31/2009
	Epitope Mapping by Combining Protein-Protein Docking and Varied Low-Resolution Structural Data
28.	S10 RR027100-01	PI
	NIH/NIGMS		04/01/2010	03/31/2011
	High Perfomance Computing Cluster for Bioimaging and Computational Biology		$ 499,512 direct/yr 1
29.	Pfizer, Inc.	PI
	California Institute for Quantitative Biosciences (QB3)		07/01/2010	06/30/2011
	A Computational Model of Allostery with Application to Antibody Design		$ 70,000 direct/yr 1	$ 70,000 total
30.	PN2 EY016525	Co-PI
	NIH		09/30/2005	09/29/2011
	Center for Protein Folding Machinery		$ 50,000 direct/yr 1	$ 600,000 total
31.	SP41 RR001081-32S1	Collaborator
	NIH		09/15/2009	09/14/2011
	Resource for Biocomputing, Visualization, and Informatics		$ 7,140 direct/yr 1	$ 14,500 total
32.		PI
	Pfizer, Inc.		10/01/2013	09/30/2014
	A Computational Model of Allostery with Application to Antibody Design		$ 55,000 direct/yr 1	$ 55,000 total
33.		PI
	Bayer Inc.		12/15/2012	12/15/2014
	Modeling of ternary MHCII-peptide-TCR complexes		$ 73,877 direct/yr 1	$ 147,755 total
34.	U01 GM61390	Collaborator
	NIH/NIGMS		04/01/2003	06/30/2015
	Pharmacogenetics of Membrane Transporters		$ 45,000 direct/yr 1	$ 600,000 total
35.	U54 GM0094625	Co-PI
	NIH/NIGMS		07/01/2005	06/30/2015
	CSMP: Centers for Membrane Protein Structure Determination		$ 65,000 direct/yr 1	$ 650,000 total
36.	U54 GM093342	Co-PI
	NIH/NIGMS		04/01/2010	04/30/2015
	Collaborative Center for an Enzyme Function Initiative		$ 170,000 direct/yr 1	$ 850,000 total
37.	U01 GM098256	Co-PI
	NIH/NIGMS		07/01/2011	07/31/2015
	Nucleocytoplasmic Transport: A Target for Cellular Control		$ 50,000 direct/yr 1	$ 200,000 total
38.	U54 GM094662	Co-PI
	NIH/NIGMS		07/01/2010	06/30/2015
	New York Structural Genomics Research Consortium		$ 150,000 direct/yr 1	$ 750,000 total
39.	R21	coPI		Charly Craik (PI)
	NIH		4/1/2014	3/31/2016
	Extracellular Proteolysis as a Molecular Stratification Tool for Cancer		$ 20000 direct/yr 1	$ 40000 total
	The goal is to apply machine learning to cancer proteolysis data sets.
40.		PI		Andrej Sali (PI)
	QB3		1/1/2014	12/31/2015
	Small molecular activators of the 20S proteasome		$ 125000 direct/yr 1	$ 225000 total
	The goal is to find small molecules that activate the human 20S proteasome.
41.	P01 AI09575	Co-PI		Sali (PI)
	NIH/NIGMS		07/13/2011	06/30/2016
	Protein Homeostasis Mechanism Underlying Enterovirus Replication and Evolution		$ 130,000 direct/yr 1	$ 650,000 total
42.	S10OD021596	PI		Sali (PI)
	NIH		07/01/2016	06/30/2017
	High Performance Computer for Computational Biosciences		$ 443,460 direct/yr 1	$ 443,460 total
	Equipment grant for high performance computer for computational bioscience.
43.	R01GM117370	CoPi		Taatjes (PI)
	NIH		01/01/2017	03/31/2018
	Mediator kinases and transcription regulation		$ 33,000 direct/yr 1
	This collaborative project seeks to gain a deep mechanistic understanding of the Mediator kinases (CDK8 and CDK19) and the CDK8 module study CDK8 and CDK19 function in the context of serum response signaling, which is fundamentally important for cell physiology, development, and cancer biology.
44.	R01GM117370	Co-Investigator		Taatjes (PI)
	University of CO, Boulder/NIH/NIGMS		04/01/2017	03/31/2020
	Mediator Kinases and Transcription Regulation
	The goal is to compute integrative structures of the Mediator complexes within the scope of the project.
45.	USC Fellowship Subcontract	PI		Sali (PI)
	NIH/NIGMS		09/01/2017	08/31/2019
	Integrative Modeling of the Human Pancreatic Beta Cell
	This award primarily supports a Postdoc. Goal is to develop and apply computer modeling for a combined experimental and computational effort on mapping the pancreatic beta cell.
46.	HARC P50			Webb (PI)
	HARC		09/01/2017	08/31/2019
	Integrative Modeling of HIV-Human Protein Complexes		$ 63,046 direct/yr 1
	Integrative Modeling of HIV-Human Protein Complexes
47.	P01 GM105537	Co-Investigator		Winey (PI)
	NIH		09/01/2014	08/31/2019
	The Yeast Centrosome-Structure, Assembly & Function		$ 135,000 direct/yr 1	$ 750,000 total
	The goal of this project is to understand the structure and function of centrosomes.
48.	P01 GM111126	Co-Investigator		Stroud (PI)
	NIH		08/01/2015	07/31/2020
	Mapping the conformational cycle of transmembrane transporters		$ 200,000 direct/yr 1	$ 1,000,000 total
	The goal is to apply integrative structure determination to select ABC transporters.
49.	U54DK107981	Co-Investigator		Alber (PI)
	NIH/NIDDK
	Mapping the 3D Genome Landscape		$ 79,701 direct/yr 1	$ 398,505 total
	The aim is to upgrade IMP to allow for mapping the three-dimensional organization of the genome.
50.	P01 GM118303	Co-Investigator		Gerlt (PI)
	University of Illinois/NIH/NIGMS		04/01/2016	06/30/2021
	Discovery of Microbial Metabolic Pathways Guided by Ligand Binding		$ 78,768 direct/yr 1
	Program project focuses on the development and application of novel computational and experimental strategies for the discovery of novel metabolic pathways in microbial species for which complete genome sequences are available.
51.	P50GM082250	Co-investigator		Krogan (PI)
	NIH/NIGMS		09/01/2017	08/31/2022
	HARC Center: HIV Accessory and Regulatory Complexes (Core 5)
	The overall goal of the Integrative Modeling Core is to facilitate the analysis and interpretation of multiple datatypes to identify and characterize the cellular proteins and networks that influence HIV virus replication.
52.	P50AI150476	Co-Investigator	7.2% % effort	Krogan (PI)
	NIAID		09/01/2017	08/31/2022
	HARC Center: HIV Accessory and Regulatory Complexes		$ 195,000 direct/yr 1
	The goal is to apply integrative structure modeling to the HIV-human protein complexes
53.	U19AI135990	Co investigator	7.2% % effort	Krogan (PI)
	NIH/NIAID		08/01/2018	07/31/2022
	HPMI - Host Pathogen Map Initiative		$ 201,000 direct/yr 1
	The goal is to apply intergrative structure modeling to host-pathogen complexes identified by the consortium.
54.	DBI 1756250	Principal Investigator	1% % effort	Sali (PI)
	National Science Foundation		09/01/2018	08/31/2022
	Collaborative Research: ABI Development: Building a Pipeline for Validation, Curation and Archiving of Integrative/Hybrid Models		$ 178,000 direct/yr 1
	The goal is to develop new methods for validating integrative structures.
55.	DBI 2112967	PI	5 % effort	Sali (PI)
	National Science Foundation		09/01/2021	08/31/2024
	Collaborative Research: Creating mechanisms to make integrative structures of large macromolecular assemblies available from the Protein Data Bank			$ 690,000 total
	This proposal aims to develop and implement methods for assessing integrative structures, develop a workflow to deposit, curate, validate, and archive integrative structures in the wwPDB data processing system, and create a mechanism to support automated deposition of integrative structures from the IM data harvesting system to the IM workflow in the wwPDB data processing system.

PEER REVIEWED PUBLICATIONS

1.

1985

M. Renko, A. Sali, V. Turk, M. Pokomy, I. Kregar. "A neutral metalloproteinase from Streptomyces rimosus." Vestnik Slovenskega Kemijskega Drustva 32/2, 161-173, 1985.

2.

1985

B. Lenarcic, A. Ritonja, A. Sali, M. Kotnik, V. Turk, W. Machleidt. "Properties and structure of human spleen stefin B - a low molecular weight protein inhibitor of cysteine proteinases." In: Cysteine Proteinases and Their Inhibitors; First International Symposium, Portoroz, Yugoslavia, September 15-18, 1985. Xvi+846p. Ed: V. Turk, pp. 473-488, Walter De Gruyter and Co., Berlin, West Germany; New York, New York, USA., 1986.

3.

1985

V. Turk, J. Brzin, B. Lenarcic, A. Sali, W. Machleidt. "Human stefins and cystatis: their properties and structural relationships." In: Cysteine Proteinases and Their Inhibitors; First International Symposium, Portoroz, Yugoslavia, September 15-18, 1985. Xvi+846p. Ed: V. Turk, pp. 429-442, Walter De Gruyter and Co., Berlin, West Germany; New York, New York, USA., 1986.

4.

1987

M. Kotnik, A. Sali, J. Kos, B. Turk, V. Turk. "Nova metoda za hitro dolocanje kineticnih konstant pri interakciji encima s kompetitivnim inhibitorjem (A new method for rapid determination of kinetic constants for competitive inhibition of enzymes)." Vestnik Slovenskaga Kemijskega Drustva 34, 369-377, 1987.

5.

1987

A. Sali, V. Turk. "Prediction of the secondary structures of stefins and cystatins, the low-molecular mass protein inhibitors of cysteine proteinases." Biol Chem Hoppe Seyler 368, 493-499, 1987.

6.

1988

T. Lah, I. Kregar, A. Sali, B. Lenarcic, M. Kotnik, V. Kostka, V. Turk. "Circular dichroism studies of different aspartyl proteinases and their interactions with pepstatin." Periodicum Biologorum 90, 31-38, 1988.

7.

1989

V. Turk, R. Jerala, B. Lenarcic, A. Sali. "Structural and functional aspects of human cathepsins B." In: Intracellular Proteolysis: Mechanisms and Regulations. Ed: N. Katunuma, E. Kominami, pp. 27 -37, Japan Scientific Societies Press, Berlin, West Germany; New York, New York, USA., 1989.

8.

1989

A. Sali, B. Veerapandian, J.B. Cooper, S.I. Foundling, D.J. Hoover, T.L. Blundell. "High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor: the analysis of the inhibitor binding and description of the rigid body shift in the enzyme." Embo Journal 8, 2179-2188, 1989.

9.

1989

T.L. Blundell, G. Elliott, S.P. Gardner, T. Hubbard, S. Islam, M. Johnson, D. Mantafounis, P. Murrayrust, J. Overington, J.E. Pitts, A. Sali, B.L. Sibanda, J. Singh, M.J.E. Sternberg, M.J. Sutcliffe, J.M. Thornton, P. Travers. "Protein engineering and design." Philosophical Transactions of the Royal Society of London Series B-Biological Sciences 324, 447-460, 1989.

10.

1988

T.L. Blundell, D. Carney, T. Hubbard, M.S. Johnson, A. McLeod, J.P. Overington, A. Sali, M.S. Sutcliffe, P. Thomas. "Knowledge-based protein modelling and design." In: Advances in Protein Design: International Workshop 1988 GBF Monographs. Ed: H. Bloecker, J. Collins, R.D. Schmid, D. Schomburg, 12, pp. 39-43, VCH, London, UK, 1989.

11.

1990

A. Sali, T.L. Blundell. "Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming." J Mol Biol 212, 403-428, 1990.

12.

1990

A. Sali, J.P. Overington, M.S. Johnson, T.L. Blundell. "From Comparisons of protein sequences and structures to protein modelling and design." Trends Biochem Sci 15, 235-240, 1990.

13.

1990

B. Veerapandian, J.B. Cooper, A. Sali, T.L. Blundell. "X-ray analyses of aspartic proteinases. III Three-dimensional structure of endothiapepsin complexed with a transition-state isostere inhibitor of renin at 1.6 A resolution." J Mol Biol 216, 1017-1029, 1990.

14.

1990

J. Overington, M.S. Johnson, A. Sali, T.L. Blundell. "Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction." Procedures in Biological Science 241, 132-145, 1990.

15.

1990

J.P. Overington, M.S. Johnson, C. Topham, A. McLeod, A. Sali, Z.Y. Zhu, L. Sibanda, T.L. Blundell. "Applications of environment specific amino acid substitution tables to identification of key residues in protein tertiary structure." Curr Sci 59, 867-874, 1990.

16.

1990

M.S. Johnson, A. Sali, T.L. Blundell. "Phylogenetic relationships from three-dimensional protein structures." Methods Enzymol 183, 670-690, 1990.

17.

1990

M.S. Johnson, J.P. Overington, A. Sali. "Knowledge-based protein modelling: Human plasma kallikrein and human neutrophil defensin." In: Chemistry: Techniques Structure and Function. Ed: J.J. Vilafranca, pp. 567-574, Academic Press, Inc., London, 1990.

18.

1990

M.S. Johnson, J. Overington, A. Sali, Z. Zhu, D. Donnelly, P. Thomas, A. McLeod, R. Goold, C. Topham, T.L. Blundell. "From comparative structure analysis to protein engineering: Knowledge-based protein modelling and design." Fresenius Journal of Analytic Chemistry 337, 1-3, 1990.

19.

1990

T.L. Blundell, M.S. Johnson, J.P. Overington, A. Sali. "Knowledge-based protein modeling and the design of novel molecules." In: Protein design and the development of new therapeutics and vaccines. Ed: J.B. Hook, G. Poste, pp. 209-227, Plenum Press, New York, NY, 1990.

20.

1991

T.L. Blundell, J.B. Cooper, A. Sali, Z.Y. Zhu. "Comparisons of the sequences, 3-D structures and mechanisms of pepsin-like and retroviral aspartic proteinases." Adv Exp Med Biol 306, 443-453, 1991.

21.

1991

T.L. Blundell, J.B. Cooper, D. Donnelly, H. Driessen, Y. Edwards, F. Eisenmenger, C. Frazao, M. Johnson, K. Niefind, M. Newman, J. Overington, A. Sali, C. Slingsby, V. Nalini, Z.Y. Zhu. "Patterns of sequence variation in families of homologous proteins." In: Methods in Protein Sequence Analysis. Ed: H. Jornval, J.O. Hoog, A.M. Gustavsson, pp. 373-385, Birkhauser Verlag, Basel, Switzerland, 1991.

22.

1991

A. Sali, J.P. Overington, M.S. Johnson, T.L. Blundell. "From modelling homologous proteins to prediction of structure." In: Protein design and the development of new therapeutics and vaccines. Ed: J.M. Goodfellow, D.S. Moss, pp. 231-245, Ellis Horwood Ltd., LYNGBY, DENMARK, 1991.

23.

1992

A. Sali, B. Veerapandian, J.B. Cooper, D.S. Moss, T. Hofmann, T.L. Blundell. "Domain flexibility in aspartic proteinases." Proteins 12, 158-170, 1992.

24.

1992

B. Veerapandian, J.B. Cooper, A. Sali, T.L. Blundell, R.L. Rosati, B.W. Dominy, D.B. Damon, D.J. Hoover. "Direct observation by X-ray analysis of the tetrahedral "intermediate" of aspartic proteinases." Protein Sci 1, 322-328, 1992.

25.

1992

Z.Y. Zhu, A. Sali, T.L. Blundell. "A variable gap penalty function and feature weights for protein 3-D structure comparisons." Protein Eng 5, 43-51, 1992.

26.

1992

J. Overington, D. Donnelly, M.S. Johnson, A. Sali, T.L. Blundell. "Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds." Protein Sci 1, 216-226, 1992.

27.

1992

M.S. Johnson, J.P. Overington, A. Sali, T.L. Blundell. "From the comparative analysis of proteins to similarity-based modelling." In: Computer Modelling of Biomolecular Processes. Ed: V.A. Ratner, N.A. Kolchanov, pp. 191-196, Nova Science Publishers, London, 1992.

28.

1993

J.P. Overington, Z.Y. Zhu, A. Sali, M.S. Johnson, R. Sowdhamini, G.V. Louie, T.L. Blundell. "Molecular recognition in protein families: a database of aligned three-dimensional structures of related proteins." Biochem Soc Trans 21 ( Pt 3), 597-604, 1993.

29.

1993

A. Sali, T.L. Blundell. "Comparative protein modelling by satisfaction of spatial restraints." J Mol Biol 234, 779-815, 1993.

30.

1993

A. Sali, R. Matsumoto, H.P. McNeil, M. Karplus, R.L. Stevens. "Three-dimensional models of four mouse mast cell chymases. Identification of proteoglycan-binding regions and protease-specific antigenic epitopes." J Biol Chem 268, 9023-9034, 1993.

31.

1994

A. Sali, T. Blundell. "Comparative protein modeling by statisfaction of spatial restraints." In: Protein Structure by Distance Analysis. Ed: H. Bohr, S. Brunak, pp. 64-86, TECH UNIV DENMARK, CTR BIOL SEQUENCE ANAL, LYNGBY, DENMARK, 1994.

32.

1994

A. Sali, J.P. Overington. "Derivation of rules for comparative protein modeling from a database of protein structure alignments." Protein Sci 3, 1582-1596, 1994.

33.

1994

A. Sali, E. Shakhnovich, M. Karplus. "Kinetics of protein folding. A lattice model study of the requirements for folding to the native state." J Mol Biol 235, 1614-1636, 1994.

34.

1994

A. Sali, E. Shakhnovich, M. Karplus. "How does a protein fold?" Nature 369, 248-251, 1994.

35.

1994

A. Dinner, A. Sali, M. Karplus, E. Shakhnovich. "Phase diagram of a model protein derived by exhaustive enumeration of the conformations." J Chem Phys 101, 1444-1451, 1994.

36.

1995

M. Karplus, A. Sali. "Theoretical studies of protein folding and unfolding." Curr Opin Struct Biol 5, 58-73, 1995.

37.

1995

M. Karplus, A. Caflisch, A. Sali, E. Shakhnovich. "Protein dynamics: From the native to the unfolded state and back again." In: Modelling of Biomolecular Structures and Mechanisms. Ed: A.Pullmanet al, pp. 69-84, Kluwer Academic Publishers, London, 1995.

38.

1995

A. Sali. "MODELLER: Implementing 3D protein modeling." In: mc^2, 2, pp. 5, Molecular Simulations Inc., Totowa, NJ, 1995.

39.

1995

X.D. Wu, B. Knudsen, S.M. Feller, J. Zheng, A. Sali, D. Cowburn, H. Hanafusa, J. Kuriyan. "Structural basis for the specific interaction of lysine-containing proline-rich peptides with the amino-terminal SH3 domain of c-Crk." Structure 3, 215-226, 1995.

40.

1995

R. Matsumoto, A. Sali, N. Ghildyal, M. Karplus, R.L. Stevens. "Packaging of proteases and proteoglycans in the granules of mast cells and other hematopoietic cells. A cluster of histidines on mouse mast cell protease 7 regulates its binding to heparin serglycin proteoglycans." J Biol Chem 270, 19524-19531, 1995.

41.

1995

A. Sali. "Comparative protein modeling by satisfaction of spatial restraints." Mol Med Today 1, 270-277, 1995.

42.

1995

A. Sali, E. Shakhnovich, M. Karplus. "Protein Folding Studied by Monte Carlo Simulations." In: Protein Folds: A Distance Based Approach. Ed: H. Bohr, S. Brunak, pp. 202-216, CRC Press Inc., LYNGBY, DENMARK, 1995.

43.

1995

A. Sali, E. Shakhnovich, M. Karplus. "Thermodynamics and kinetics of protein folding from lattice Monte Carlo simulations." In: DIMACS Series in Discrete Mathematics and Theoretical Computer Science. Ed: D. Shalloway, G. Xue, P. Pardalos, 23, pp. 199-213, American Mathematical Society, LYNGBY, DENMARK, 1995.

44.

1995

A. Sali, L. Potterton, F. Yuan, H. van Vlijmen, M. Karplus. "Evaluation of comparative protein modeling by MODELLER." Proteins 23, 318-326, 1995.

45.

1995

A. Sali. "Modeling mutations and homologous proteins." Curr Opin Biotechnol 6, 437-451, 1995.

46.

1995

M. Karplus, A. Sali, E. Shakhnovich. "Kinetics of protein folding." Nature 373, 664-665, 1995.

47.

1996

Y. Sheng, A. Sali, H. Herzog, J. Lahnstein, S.A. Krilis. "Site-directed mutagenesis of recombinant human beta 2-glycoprotein I identifies a cluster of lysine residues that are critical for phospholipid binding and anti-cardiolipin antibody activity." J Immunol 157, 3744-3751, 1996.

48.

1996

N. Ghildyal, D.S. Friend, R.L. Stevens, K.F. Austen, C. Huang, J.F. Penrose, A. Sali, M.F. Gurish. "Fate of two mast cell tryptases in V3 mastocytosis and normal BALB/c mice undergoing passive systemic anaphylaxis: prolonged retention of exocytosed mMCP-6 in connective tissues, and rapid accumulation of enzymatically active mMCP-7 in the blood." The Journal of Experimental Medicine 184, 1061-1073, 1996.

49.

1996

L.Z. Xu, R. Sanchez, A. Sali, N. Heintz. "Ligand specificity of brain lipid-binding protein." J Biol Chem 271, 24711-24719, 1996.

50.

1996

A.R. Dinner, A. Sali, M. Karplus. "The folding mechanism of larger model proteins: role of native structure." Proc Natl Acad Sci U S A 93, 8356-8361, 1996.

51.

1996

S. Wu, H. de Lencastre, A. Sali, A. Tomasz. "A phosphoglucomutase-like gene essential for the optimal expression of methicillin resistance in Staphylococcus aureus: molecular cloning and DNA sequencing." Microbial Drug Resistance 2, 277-286, 1996.

52.

1997

M. Russel, N.A. Linderoth, A. Sali. "Filamentous phage assembly: variation on a protein export theme." Gene 192, 23-32, 1997.

53.

1997

C. Huang, G.W. Wong, N. Ghildyal, M.F. Gurish, A. Sali, R. Matsumoto, W.T. Qiu, R.L. Stevens. "The tryptase, mouse mast cell protease 7, exhibits anticoagulant activity in vivo and in vitro due to its ability to degrade fibrinogen in the presence of the diverse array of protease inhibitors in plasma." J Biol Chem 272, 31885-31893, 1997.

54.

1997

R. Sanchez, A. Sali. "Comparative protein modeling as an optimization problem." Journal of Molecular Structure (Theochem) 398, 489-496, 1997.

55.

1997

R. Sanchez, A. Sali. "Advances in comparative protein-structure modelling." Curr Opin Struct Biol 7, 206-214, 1997.

56.

1997

D. Koulich, M. Orlova, A. Malhotra, A. Sali, S.A. Darst, S. Borukhov. "Domain organization of Escherichia coli transcript cleavage factors GreA and GreB." J Biol Chem 272, 7201-7210, 1997.

57.

1997

J.E. Hunt, D.S. Friend, M.F. Gurish, E. Feyfant, A. Sali, C. Huang, N. Ghildyal, S. Stechschulte, K.F. Austen, R.L. Stevens. "Mouse mast cell protease 9, a novel member of the chromosome 14 family of serine proteases that is selectively expressed in uterine mast cells." J Biol Chem 272, 29158-29166, 1997.

58.

1997

R. Sanchez, A. Sali. "Evaluation of comparative protein structure modeling by MODELLER-3." Proteins Suppl 1, 50-58, 1997.

59.

1997

B. Guenther, R. Onrust, A. Sali, M. O'Donnell, J. Kuriyan. "Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III." Cell 91, 335-345, 1997.

60.

1997

R. Sanchez, A.Ya. Badretdinov, E. Feyfant, A. Sali. "Homology protein structure modeling." Transactions of the American Crystallographic Association 32, 81-91, 1997.

61.

1997

Y. Sheng, S.A. Krilis, A. Sali. "Site-directed mutagenesis of recombinant human beta 2-glycoprotein I. Effect of phospholipid binding and anticardiolipin antibody activity." Ann N Y Acad Sci 815, 331-333, 1997.

62.

1998

C.M. Dobson, A. Sali, M. Karplus. "Protein folding: A perspective from theory and experiment." Angewandte Chemie Int Ed 37, 868-893, 1998.

63.

1998

C. Huang, A. Sali, R.L. Stevens. "Regulation and function of mast cell proteases in inflammation." J Clin Immunol 18, 169-183, 1998.

64.

1998

D.A. Kandiah, A. Sali, Y. Sheng, E.J. Victoria, D.M. Marquis, S.M. Coutts, S.A. Krilis. "Current insights into the "antiphospholipid" syndrome: clinical, immunological, and molecular aspects." Advanced Immunology Journal 70, 507-563, 1998.

65.

1998

A. Gutin, A. Sali, V. Abkevich, M. Karplus, E. Shakhnovich. "Temperature dependence of the folding rate in a simple protein model: Search for a glass transition." J Chem Phys 108, 6466-6483, 1998.

66.

1998

E. Wolf, A. Vassilev, Y. Makino, A. Sali, Y. Nakatani, S.K. Burley. "Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase." Cell 94, 439-449, 1998.

67.

1998

R. Sanchez, A. Sali. "Large-scale protein structure modeling of the Saccharomyces cerevisiae genome." Proc Natl Acad Sci U S A 95, 13597-13602, 1998.

68.

1998

A. Sali. "100,000 protein structures for the biologist." Nat Struct Biol 5, 1029-1032, 1998.

69.

1999

R. Sanchez, A. Sali. "MODBASE: A database of comparative protein structure models." Bioinformatics 15, 1060-1061, 1999.

70.

1999

R. Sanchez, A. Sali. "Comparative protein structure modeling in genomics." Journal of Computational Physics 151, 388-401, 1999.

71.

1999

G. Wu, A. Fiser, B. ter Kuile, A. Sali, M. Muller. "Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase." Proc Natl Acad Sci U S A 96, 6285-6290, 1999.

72.

1999

T. Nagata, V. Gupta, D. Sorce, W.Y. Kim, A. Sali, B.T. Chait, K. Shigesada, Y. Ito, M.H. Werner. "Immunoglobulin motif DNA recognition and heterodimerization of the PEBP2/CBF Runt domain." Nat Struct Biol 6, 615-619, 1999.

73.

1999

J.M. Miwa, I. Ibanez-Tallon, G.W. Crabtree, R. Sanchez, A. Sali, L.W. Role, N. Heintz. "lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine receptors in the mammalian CNS." Neuron 23, 105-114, 1999.

74.

1999

G.W. Wong, Y. Tang, E. Feyfant, A. Sali, L. Li, Y. Li, C. Huang, D.S. Friend, S.A. Krilis, R.L. Stevens. "Identification of a new member of the tryptase family of mouse and human mast cell proteases which possesses a novel COOH-terminal hydrophobic extension." J Biol Chem 274, 30784-30793, 1999.

75.

1999

S.K. Burley, S.C. Almo, J.B. Bonanno, M. Capel, M.R. Chance, T. Gaasterland, D. Lin, A. Sali, F.W. Studier, S. Swaminathan. "Structural genomics: beyond the human genome project." Nat Genet 23, 151-157, 1999.

76.

1999

A. Sali, J. Kuriyan. "Challenges at the frontiers of structural biology (Reprinted from Trends in Biochemical Science, vol 12, Dec., 1999)." Trends Cell Biol 9, M20-M24, 1999.

77.

1999

A. Sali. "Functional links between proteins." Nature 402, 23, 25-26, 1999.

78.

1999

P. Baldi, M. Borodovsky, S. Brunak, C. Burge, J. Fickett, S. Henikoff, E. Koonin, A. Sali, C. Sander, G. Stormo. "The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function." Bioinformatics 15, 865-866, 1999.

79.

2000

C. Huang, G. Morales, A. Vagi, K. Chanasyk, M. Ferrazzi, C. Burklow, W.T. Qiu, E. Feyfant, A. Sali, R.L. Stevens. "Formation of enzymatically active, homotypic, and heterotypic tetramers of mouse mast cell tryptases. Dependence on a conserved Trp-rich domain on the surface." J Biol Chem 275, 351-358, 2000.

80.

2000

M.A. Marti-Renom, A.C. Stuart, A. Fiser, R. Sanchez, F. Melo, A. Sali. "Comparative protein structure modeling of genes and genomes." Annu Rev Biophys Biomol Struct 29, 291-325, 2000.

81.

2000

R. Sanchez, U. Pieper, N. Mirkovic, P.I.W. de Bakker, E. Wittenstein, A. Sali. "ModBase, a database of annotated comparative protein structure models." Nucleic Acids Res 28, 250-253, 2000.

82.

2000

A.R. Dinner, A. Sali, L.J. Smith, C.M. Dobson, M. Karplus. "Understanding protein folding via free-energy surfaces from theory and experiment." Trends Biochem Sci 25, 331-339, 2000.

83.

2000

R. Sanchez, A. Sali. "Comparative protein structure modeling. Introduction and practical examples with modeller." Methods Mol Biol 143, 97-129, 2000.

84.

2000

G. Wu, A.G. McArthur, A. Fiser, A. Sali, M.L. Sogin, M. Muller. "Core histones of the amitochondriate protist, Giardia lamblia." Mol Biol Evol 17, 1156-1163, 2000.

85.

2000

A. Fiser, R.K.G. Do, A. Sali. "Modeling of loops in protein structures." Protein Sci 9, 1753-1773, 2000.

86.

2000

W. Liedtke, Y. Choe, M.A. Marti-Renom, A.M. Bell, C.S. Denis, A. Sali, A.J. Hudspeth, J.M. Friedman, S. Heller. "Vanilloid receptor-related osmotically activated channel (VR-OAC), a candidate vertebrate osmoreceptor." Cell 103, 525-535, 2000.

87.

2000

S.K. Jin, S. Martinek, W.S. Joo, J.R. Wortman, N. Mirkovic, A. Sali, M.D. Yandell, N.P. Pavletich, M.W. Young, A.J. Levine. "Identification and characterization of a p53 homologue in Drosophila melanogaster." Proc Natl Acad Sci U S A 97, 7301-7306, 2000.

88.

2000

R. Sanchez, U. Pieper, F. Melo, N. Eswar, M.A. Marti-Renom, M.S. Madhusudhan, N. Mirkovic, A. Sali. "Protein structure modeling for structural genomics." Nat Struct Biol 7, 986-990, 2000.

89.

2000

A. Fiser, R. Sanchez, F. Melo, A. Sali. "Comparative protein structure modeling." In: Computational Biochemistry and Biophysics. Ed: M. Watanabe, B. Roux, A. Mackerell, O. Becker, pp. 275-312, Marcel Dekker, Oxford, UK, 2000.

90.

2000

C.M. Groft, R. Beckmann, A. Sali, S.K. Burley. "Crystal structures of ribosome anti-association factor IF6." Nat Struct Biol 7, 1156-1164, 2000.

91.

2001

S. Gopal, M. Schroeder, U. Pieper, A. Sczyrba, G. Aytekin-Kurban, S. Bekiranov, J.E. Fajardo, N. Eswar, R. Sanchez, A. Sali, T. Gaasterland. "Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome." Nat Genet 27, 337-340, 2001.

92.

2001

V.A. Eyrich, M.A. Marti-Renom, D. Przybylski, M.S. Madhusudhan, A. Fiser, F. Pazos, A. Valencia, A. Sali, B. Rost. "EVA: continuous automatic evaluation of protein structure prediction servers." Bioinformatics 17, 1242-1243, 2001.

93.

2001

M.A. Marti-Renom, V.A. Ilyin, A. Sali. "DBAli: a database of protein structure alignments." Bioinformatics 17, 746-747, 2001.

94.

2001

G.W. Wong, L. Li, M.S. Madhusudhan, S.A. Krilis, M.F. Gurish, M.E. Rothenberg, A. Sali, R.L. Stevens. "Tryptase 4, a new member of the chromosome 17 family of mouse serine proteases." J Biol Chem 276, 20648-20658, 2001.

95.

2001

L.G. Barrientos, R. Campos-Olivas, J.M. Louis, A. Fiser, A. Sali, A.M. Gronenborn. "1H, 13C, 15N resonance assignments and fold verification of a circular permuted variant of the potent HIV-inactivating protein cyanovirin-N." J Biomol NMR 19, 289-290, 2001.

96.

2001

A. Sali. "Target practice." Nat Struct Biol 8, 482-484, 2001.

97.

2001

J.B. Bonanno, C. Edo, N. Eswar, U. Pieper, M.J. Romanowski, V. Ilyin, S.E. Gerchman, H. Kycia, F.W. Studier, A. Sali, S.K. Burley. "Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis." Proc Natl Acad Sci U S A 98, 12896-12901, 2001.

98.

2001

C.M. Spahn, R. Beckmann, N. Eswar, P.A. Penczek, A. Sali, G. Blobel, J. Frank. "Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions." Cell 107, 373-386, 2001.

99.

2001

R. Beckmann, C.M.T. Spahn, N. Eswar, J. Helmers, P.A. Penczek, A. Sali, J. Frank, G. Blobel. "Architecture of the protein-conducting channel associated with the translating 80S ribosome." Cell 107, 361-372, 2001.

100.

2001

G.W. Wong, S. Yasuda, M.S. Madhusudhan, L. Li, Y. Yang, S.A. Krilis, A. Sali, R.L. Stevens. "Human tryptase epsilon (PRSS22), a new member of the chromosome 16p13.3 family of human serine proteases expressed in airway epithelial cells." J Biol Chem 276, 49169-49182, 2001.

101.

2001

M. Borodovsky, E. Koonin, C. Burge, J. Fickett, J. Logsdon, A. Sali, G. Stormo, I. Zhulin. "The third Georgia Tech - Emory international conference on bioinformatics: in silico biology; bioinformatics after human genome November 15-18, 2001, Atlanta, Georgia, USA." Bioinformatics 17, 859-861, 2001.

102.

2001

C.M. Groft, R. Beckmann, A. Sali, S.K. Burley. "Response to Paoli." Nat Struct Biol 8, 745, 2001.

103.

2001

D. Baker, A. Sali. "Protein structure prediction and structural genomics." Science 294, 93-96, 2001.

104.

2002

J. Vernal, A. Fiser, A. Sali, M. Muller, J.J. Cazzulo, C. Nowicki. "Probing the specificity of a trypanosomal aromatic alpha-hydroxy acid dehydrogenase by site-directed mutagenesis." Biochem Biophys Res Commun 293, 633-639, 2002.

105.

2002

F. Melo, R. Sanchez, A. Sali. "Statistical potentials for fold assessment." Protein Sci 11, 430-448, 2002.

106.

2002

A.C. Stuart, V.A. Ilyin, A. Sali. "LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures." Bioinformatics 18, 200-201, 2002.

107.

2002

M.A. Marti-Renom, M.S. Madhusudhan, A. Fiser, B. Rost, A. Sali. "Reliability of assessment of protein structure prediction methods." Structure 10, 435-440, 2002.

108.

2002

A. Sali, M.A. Marti-Renom, M.S. Madhusudhan, A. Fiser, B. Rost. "Reply to Moult et al." Structure 10, 292-293, 2002.

109.

2002

A. Fiser, M. Feig, C.L. Brooks, A. Sali. "Evolution and physics in comparative protein structure modeling." Accounts of Chemical Research 35, 413-421, 2002.

110.

2002

U. Pieper, N. Eswar, A.C. Stuart, V.A. Ilyin, A. Sali. "MODBASE, a database of annotated comparative protein structure models." Nucleic Acids Res 30, 255-259, 2002.

111.

2002

M.R. Chance, A.R. Bresnick, S.K. Burley, J.S. Jiang, C.D. Lima, A. Sali, S.C. Almo, J.B. Bonanno, J.A. Buglino, S. Boulton, H. Chen, N. Eswar, G.S. He, R. Huang, V. Ilyin, L. McMahan, U. Pieper, S. Ray, M. Vidal, L.K. Wang. "Structural genomics: A pipeline for providing structures for the biologist." Protein Sci 11, 723-738, 2002.

112.

2001

K.R. Rajashankar, M.R. Chance, S.K. Burley, J. Jiang, S.C. Almo, A.R. Bresnick, T. Dodatko, R. Huang, G. He, H. Chen, M. Sullivan, J. Toomey, R.A. Thirumuruhan, W.A. Franklin, A. Sali, U. Pieper, N. Eswar, V. Ilyin, L. McMahan. "Structural Genomics at the National Synchrotron Light Source." NSLS Activity Report 2001 2, 28-32, 2002.

113.

2002

Y. Yang, L.X. Li, G.W. Wong, S.A. Krilis, M.S. Madhusudhan, A. Sali, R.L. Stevens. "RasGRP4, a new mast cell-restricted Ras guanine nucleotide-releasing protein with calcium- and diacylglycerol-binding motifs - Identification of defective variants of this signaling protein in asthma, mastocytosis, and mast cell leukemia patients and demonstration of the importance of RasGRP4 in mast cell development and function." J Biol Chem 277, 25756-25774, 2002.

114.

2002

M.A. Marti-Renom, B. Yerkovich, A. Sali. "Comparative protein structure prediction." In: Current Protocols in Protein Science, pp. 2.9.1-2.9.22, John Wiley & Sons, Totowa, NJ, 2002.

115.

2002

G.M. Iverson, S. Reddel, E.J. Victoria, K.A. Cockerill, Y.X. Wang, M.A. Marti-Renom, A. Sali, D.M. Marquis, S.A. Krilis, M.D. Linnik. "Use of single point mutations in domain I of beta(2)-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies." J Immunol 169, 7097-7103, 2002.

116.

2003

A. Fiser, A. Sali. "Modeller: generation and refinement of homology-based protein structure models." Methods Enzymol 374, 461-491, 2003.

117.

2003

V.A. Ilyin, U. Pieper, A.C. Stuart, M.A. Marti-Renom, L. McMahan, A. Sali. "ModView, visualization of multiple protein sequences and structures." Bioinformatics 19, 165-166, 2003.

118.

2003

M.A. Marti-Renom, B. Yerkovich, A. Sali. "Modeling protein structure from its sequence." In: Current Protocols in Bioinformatics, V. 5 January Issue, pp. 5.1.1-5.1.32, John Wiley & Sons, Inc., Hoboken, NJ, Totowa, NJ, 2003.

119.

2003

A. Fiser, A. Sali. "Comparative Protein Structure Modeling." In: Protein Structure. Ed: D. Chasman, pp. 167-206, Marcel Dekker, Inc., Oxford, UK, 2003.

120.

2003

A. Sali, R. Glaeser, T. Earnest, W. Baumeister. "From words to literature in structural proteomics." Nature 422, 216-225, 2003.

121.

2003

I.Y.Y. Koh, V.A. Eyrich, M.A. Marti-Renom, D. Przybylski, M.S. Madhusudhan, N. Eswar, O. Grana, F. Pazos, A. Valencia, A. Sali, B. Rost. "EVA: evaluation of protein structure prediction servers." Nucleic Acids Res 31, 3311-3315, 2003.

122.

2003

B. John, A. Sali. "Comparative protein structure modeling by iterative alignment, model building and model assessment." Nucleic Acids Res 31, 3982-3992, 2003.

123.

2003

N. Eswar, B. John, N. Mirkovic, A. Fiser, V.A. Ilyin, U. Pieper, A.C. Stuart, M.A. Marti-Renom, M.S. Madhusudhan, B. Yerkovich, A. Sali. "Tools for comparative protein structure modeling and analysis." Nucleic Acids Res 31, 3375-3380, 2003.

124.

2003

H.X. Gao, J. Sengupta, M. Valle, A. Korostelev, N. Eswar, S.M. Stagg, P. Van Roey, R.K. Agrawal, S.C. Harvey, A. Sali, M.S. Chapman, J. Frank. "Study of the structural dynamics of the E-coli 70S ribosome using real-space refinement." Cell 113, 789-801, 2003.

125.

2003

S.A. Lee, E.L. Shen, A. Fiser, A. Sali, S. Guo. "The zebrafish forkhead transcription factor Foxi1 specifies epibranchial placode-derived sensory neurons." Development 130, 2669-2679, 2003.

126.

2003

M.A. Marti-Renom, A. Fiser, M.S. Madhusudhan, B. John, A.C. Stuart, N. Eswar, U. Pieper, M.-.Y. Shen, A. Sali. "Modeling protein structure from its sequence." In: Current Protocols in Bioinformatics, V. 5, pp. 5.1.1-5.1.32, John Wiley & Sons, Inc., Totowa, NJ, 2003.

127.

2003

A. Sali. "NIH workshop on structural proteomics of biological complexes." Structure 11, 1043-1047, 2003.

128.

2003

A. Fiser, A. Sali. "ModLoop: automated modeling of loops in protein structures." Bioinformatics 19, 2500-2501, 2003.

129.

2004

N. Mirkovic, M.A. Marti-Renom, B.L. Weber, A. Sali, A.N. Monteiro. "Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition." Cancer Res 64, 3790-3797, 2004.

130.

2004

A. Rossi, Q. Deveraux, B. Turk, A. Sali. "Comprehensive search for cysteine cathepsins in the human genome." Biol Chem 385, 363-372, 2004.

131.

2004

M.A. Marti-Renom, M.S. Madhusudhan, A. Sali. "Alignment of protein sequences by their profiles." Protein Sci 13, 1071-1087, 2004.

132.

2004

F. Alber, N. Eswar, A. Sali. "Structure determination of macromolecular complexes by experiment and computation." Practical Bioinformatics, Ed: J.Bujnicki 15, 73-96, 2004.

133.

2004

B. John, A. Sali. "Detection of homologous proteins by an intermediate sequence search." Protein Sci 13, 54-62, 2004.

134.

2004

S.M. Maurer, A. Rai, A. Sali. "Finding Cures for Tropical Diseases: Is Open Source An Answer?" Minnesota Journal of Law, Science & Technology 6, 169-175, 2004.

135.

2004

U. Pieper, N. Eswar, H. Braberg, M.S. Madhusudhan, F.P. Davis, A.C. Stuart, N. Mirkovic, A. Rossi, M.A. Marti-Renom, A. Fiser, B. Webb, D. Greenblatt, C.C. Huang, T.E. Ferrin, A. Sali. "MODBASE, a database of annotated comparative protein structure models, and associated resources." Nucleic Acids Res 32, D217-D222, 2004.

136.

2004

S.M. Maurer, A. Rai, A. Sali. "Finding Cures for Tropical Diseases: Is Open Source An Answer?" In: Biotechnology: Essays From Its Heartland. Ed: L.y.n.n. Laboratory Yarris, June 2004, pp. 33-37, John Wiley & Sons, Totowa, NJ, 2004.

137.

2004

M.R. Chance, A. Fiser, A. Sali, U. Pieper, N. Eswar, G. Xu, J.E. Fajardo, T. Radhakannan, N. Marinkovic. "High-throughput computational and experimental techniques in structural genomics." Genome Res 14, 2145-2154, 2004.

138.

2004

M. Jacobson, A. Sali. "Comparative Protein Structure Modeling and Its Applications to Drug Discovery." In: Annual Reports in Medicinal Chemistry. Ed: J. Overington, 39, pp. 259-276, Inpharmatica Ltd., London, 2004.

139.

2004

R.B. Russell, F. Alber, P. Aloy, F.P. Davis, D. Korkin, M. Pichaud, M. Topf, A. Sali. "A structural perspective on protein-protein interactions." Curr Opin Struct Biol 14, 313-324, 2004.

140.

2004

D. Devos, S. Dokudovskaya, F. Alber, R. Williams, B.T. Chait, A. Sali, M.P. Rout. "Components of coated vesicles and nuclear pore complexes share a common molecular architecture." PLoS Biology 2, e380, 2004.

141.

2004

S.M. Maurer, A. Rai, A. Sali. "Finding Cures for Tropical Diseases: Is Open Source an Answer?" PLoS Medicine 1, e56, 2004.

142.

2005

J. Espadaler, R. Aragues, N. Eswar, M.A. Marti-Renom, E. Querol, F.X. Aviles, A. Sali, B. Oliva. "Detecting remotely related proteins by their interactions and sequence similarity." Proc Natl Acad Sci U S A 102, 7151-7156, 2005.

143.

2005

M. Topf, M.L. Baker, B. John, W. Chiu, A. Sali. "Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy." J Struct Biol 149, 191-203, 2005.

144.

2005

R. Karchin, L. Kelly, A. Sali. "Improving functional annotation of non-synonomous SNPs with information theory." Pac Symp Biocomput, 397-408, 2005.

145.

2005

M.S. Madhusudhan, M.A. Marti-Renom, N. Eswar, B. John, U. Pieper, R. Karchin, M.i.n.-.y.i. Shen, A. Sali. "Comparative Protein Structure Modeling." In: Proteomics Protocols Handbook. Ed: J.M. Walker, pp. 831-860, Humana Press Inc., Totowa, NJ, 2005.

146.

2005

F. Alber, M.F. Kim, A. Sali. "Structural characterization of assemblies from overall shape and subcomplex compositions." Structure 13, 435-445, 2005.

147.

2005

F.P. Davis, A. Sali. "PIBASE: a comprehensive database of structurally defined protein interfaces." Bioinformatics 21, 1901-1907, 2005.

148.

2005

R. Karchin, M. Diekhans, L. Kelly, D.J. Thomas, U. Pieper, N. Eswar, D. Haussler, A. Sali. "LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources." Bioinformatics 21, 2814-2820, 2005.

149.

2005

S. Yasuda, N. Morokawa, G.W. Wong, A. Rossi, M.S. Madhusudhan, A. Sali, Y.S. Askew, R. Adachi, G.A. Silverman, S.A. Krilis, R.L. Stevens. "Urokinase-type plasminogen activator is a preferred substrate of the human epithelium serine protease tryptase epsilon/PRSS22." Blood 105, 3893-3901, 2005.

150.

2005

J. Dvorak, M. Delcroix, A. Rossi, V. Vopalensky, M. Pospisek, M. Sedinova, L. Mikes, M. Sajid, A. Sali, J.H. Mckerrow, P. Horak, C.R. Caffrey. "Multiple cathepsin B isoforms in schistosomula of Trichobilharzia regenti: Identification, characterization and putative role in migration and nutrition." International Journal of Parasitology 35, 895-910, 2005.

151.

2005

A. Sali, W. Chiu. "Macromolecular assemblies highlighted." Structure 13, 339-341, 2005.

152.

2005

D. Korkin, F.P. Davis, A. Sali. "Localization of protein-binding sites within families of proteins." Protein Sci 14, 2350-2360, 2005.

153.

2005

M.Y. Shen, F.P. Davis, A. Sali. "The optimal size of a globular protein domain: A simple sphere-packing model." Chem Phys Lett 405, 224-228, 2005.

154.

2005

J.B. Bonanno, S.C. Almo, A. Bresnick, M.R. Chance, A. Fiser, S. Swaminathan, J. Jiang, F.W. Studier, L. Shapiro, C.D. Lima, T.M. Gaasterland, A. Sali, K. Bain, I. Feil, X. Gao, D. Lorimer, A. Ramos, J.M. Sauder, S.R. Wasserman, S. Emtage, K.L. D'Amico, S.K. Burley. "New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative." J Struct Funct Genom 6, 225-232, 2005.

155.

2005

M. Topf, A. Sali. "Combining electron microscopy and comparative protein structure modeling." Curr Opin Struct Biol 15, 578-585, 2005.

156.

2005

S.A. McMahon, J.L. Miller, J.A. Lawton, D.E. Kerkow, A. Hodes, M.A. Marti-Renom, S. Doulatov, E. Narayanan, A. Sali, J.F. Miller, P. Ghosh. "The C-type lectin fold as an evolutionary solution for massive sequence variation." Nature Structural Molecular Biology 12, 886-892, 2005.

157.

2006

D. Devos, S. Dokudovskaya, R. Williams, F. Alber, N. Eswar, B.T. Chait, M.P. Rout, A. Sali. "Simple fold composition and modular architecture of the nuclear pore complex." Proc Natl Acad Sci U S A 103, 2172-2177, 2006.

158.

2006

M.S. Madhusudhan, M.A. Marti-Renom, R. Sanchez, A. Sali. "Variable gap penalty for protein sequence-structure alignment." Protein Engineering, Design & Selection 19, 129-133, 2006.

159.

2006

C. Lima, J. Puglisi, A. Sali, L. Szewczak. "Editorial." Structure 14, 801, 2006.

160.

2006

U. Pieper, N. Eswar, F.P. Davis, H. Braberg, M.S. Madhusudhan, A. Rossi, M. Marti-Renom, R. Karchin, B.M. Webb, D. Eramian, M.Y. Shen, L. Kelly, F. Melo, A. Sali. "MODBASE: a database of annotated comparative protein structure models and associated resources." Nucleic Acids Res 34, D291-295, 2006.

161.

2006

M. Topf, M.L. Baker, M.A. Marti-Renom, W. Chiu, A. Sali. "Refinement of protein structures by iterative comparative modeling and CryoEM density fitting." J Mol Biol 357, 1655-1668, 2006.

162.

2006

D. Korkin, F.P. Davis, F. Alber, T. Luong, M.Y. Shen, V. Lucic, M.B. Kennedy, A. Sali. "Structural modeling of protein interactions by analogy: application to PSD-95." PLoS Computational Biology 2, e153, 2006.

163.

2006

D. Eramian, M.Y. Shen, D. Devos, F. Melo, A. Sali, M.A. Marti-Renom. "A composite score for predicting errors in protein structure models." Protein Sci 15, 1653-1666, 2006.

164.

2006

S. Dokudovskaya, R. Williams, D. Devos, A. Sali, B.T. Chait, M.P. Rout. "Protease accessibility laddering: a proteomic tool for probing protein structure." Structure 14, 653-660, 2006.

165.

2006

N. Eswar, B. Webb, M.A. Marti-Renom, M.S. Madhusudhan, D. Eramian, M.Y. Shen, U. Pieper, A. Sali. "Comparative protein structure modeling using Modeller." Current Protocols in Bioinformatics Chapter 5, Unit 5.6, 2006.

166.

2006

A. Rossi, M.A. Marti-Renom, A. Sali. "Localization of binding sites in protein structures by optimization of a composite scoring function." Protein Sci 15, 2366-2380, 2006.

167.

2006

F.P. Davis, H. Braberg, M.Y. Shen, U. Pieper, A. Sali, M.S. Madhusudhan. "Protein complex compositions predicted by structural similarity." Nucleic Acids Res 34, 2943-2952, 2006.

168.

2006

T.D. Nguyen, J.M. Gow, L.W. Chinn, L. Kelly, H. Jeong, C.C. Huang, D. Stryke, M. Kawamoto, S.J. Johns, E. Carlson, T. Taylor, T.E. Ferrin, A. Sali, K.M. Giacomini, D.L. Kroetz. "PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network." Pharmacol Rev 58, 1-2, 2006.

169.

2006

H.M. Berman, S.K. Burley, W. Chiu, A. Sali, A. Adzhubei, P.E. Bourne, S.H. Bryant, R.L. Dunbrack Jr., K. Fidelis, J. Frank, A. Godzik, K. Henrick, A. Joachimiak, B. Heymann, D. Jones, J.L. Markley, J. Moult, G.T. Montelione, C. Orengo, M.G. Rossmann, B. Rost, H. Saibil, T. Schwede, D.M. Standley, J.D. Westbrook. "Outcome of a workshop on archiving structural models of biological macromolecules." Structure 14, 1211-1217, 2006.

170.

2006

A. Colubri, A.K. Jha, M.Y. Shen, A. Sali, R.S. Berry, T.R. Sosnick, K.F. Freed. "Minimalist representations and the importance of nearest neighbor effects in protein folding simulations." J Mol Biol 363, 835-857, 2006.

171.

2006

M.Y. Shen, A. Sali. "Statistical potential for assessment and prediction of protein structures." Protein Sci 15, 2507-2524, 2006.

172.

2006

N. Eswar, B. Webb, M.A. Marti-Renom, M.S. Madhusudhan, D. Eramian, M.Y. Shen, U. Pieper, A. Sali. "Comparative protein structure modeling using MODELLER." Curr Protoc Bioinformatics Chapter 5, Unit 5.6.1-5.6.30, 2006.

173.

2007

R. Karchin, A.N. Monteiro, S.V. Tavtigian, M.A. Carvalho, A. Sali. "Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning." PLoS Computational Biology 3, e26, 2007.

174.

2007

L. Kelly, R. Karchin, A. Sali. "Protein interactions and disease phenotypes in the ABC transporter superfamily." Pac Symp Biocomput, 51-63, 2007.

175.

2007

N. Eswar, A. Sali. "Comparative Modeling of Drug Target Proteins." In: Volume 4 Computer-Assisted Drug Design, Comprehensive Medicinal Chemistry II. Ed: J. Taylor, D. Triggle, J.S. Mason, pp. 215-236, Elsevier Ltd, Oxford, UK, 2007.

176.

2007

M.A. Carvalho, S.M. Marsillac, R. Karchin, S. Manoukian, S. Grist, R.F. Swaby, T.P. Urmenyi, E. Rondinelli, R. Silva, L. Gayol, L. Baumbach, R. Sutphen, J.L. Pickard-Brzosowicz, K.L. Nathanson, A. Sali, D. Goldgar, F.J. Couch, P. Radice, A.N. Monteiro. "Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis." Cancer Res 67, 1494-1501, 2007.

177.

2007

S.X. Wang, K.C. Pandey, J. Scharfstein, J. Whisstock, R.K. Huang, J. Jacobelli, R.J. Fletterick, P.J. Rosenthal, M. Abrahamson, L.S. Brinen, A. Rossi, A. Sali, J.H. McKerrow. "The structure of chagasin in complex with a cysteine protease clarifies the binding mode and evolution of an inhibitor family." Structure 15, 535-543, 2007.

178.

2007

E. Feyfant, A. Sali, A. Fiser. "Modeling mutations in protein structures." Protein Sci 16, 2030-2041, 2007.

179.

2007

N. Soranzo, L. Kelly, L. Martinian, M.W. Burley, M. Thom, A. Sali, D.L. Kroetz, D.B. Goldstein, S.M. Sisodiya. "Lack of support for a role for RLIP76 (RALBP1) in response to treatment or predisposition to epilepsy." Epilepsia 48, 674-683, 2007.

180.

2007

K. Bajaj, M.S. Madhusudhan, B.V. Adkar, P. Chakrabarti, C. Ramakrishnan, A. Sali, R. Varadarajan. "Stereochemical criteria for prediction of the effects of proline mutations on protein stability." PLoS Comput Biol 3, e241, 2007.

181.

2007

R. Aragues, A. Sali, J. Bonet, M.A. Marti-Renom, B. Oliva. "Characterization of protein hubs by inferring interacting motifs from protein interactions." PLoS Comput Biol 3, 1761-1771, 2007.

182.

2007

M.A. Marti-Renom, A. Rossi, F. Al-Shahrour, F.P. Davis, U. Pieper, J. Dopazo, A. Sali. "The AnnoLite and AnnoLyze programs for comparative annotation of protein structures." BMC Bioinformatics 8 Suppl 4, S4, 2007.

183.

2007

M.A. Marti-Renom, U. Pieper, M.S. Madhusudhan, A. Rossi, N. Eswar, F.P. Davis, F. Al-Shahrour, J. Dopazo, A. Sali. "DBAli tools: mining the protein structure space." Nucleic Acids Res 35, W393-397, 2007.

184.

2007

F.P. Davis, D.T. Barkan, N. Eswar, J.H. McKerrow, A. Sali. "Host pathogen protein interactions predicted by comparative modeling." Protein Sci 16, 2585-2596, 2007.

185.

2007

S.C. Almo, J.B. Bonanno, J.M. Sauder, S. Emtage, T.P. Dilorenzo, V. Malashkevich, S.R. Wasserman, S. Swaminathan, S. Eswaramoorthy, R. Agarwal, D. Kumaran, M. Madegowda, S. Ragumani, Y. Patskovsky, J. Alvarado, U.A. Ramagopal, J. Faber-Barata, M.R. Chance, A. Sali, A. Fiser, Z.Y. Zhang, D.S. Lawrence, S.K. Burley. "Structural genomics of protein phosphatases." J Struct Funct Genom 8, 121-140, 2007.

186.

2007

F. Melo, A. Sali. "Fold assessment for comparative protein structure modeling." Protein Sci 16, 2412-2426, 2007.

187.

2007

A. Sali, C.D. Lima, M. Kostic. "Structural genomics." Structure 15, 1341, 2007.

188.

2007

V.D. Winn, R. Haimov-Kochman, A.C. Paquet, Y.J. Yang, M.S. Madhusudhan, M. Gormley, K.T. Feng, D.A. Bernlohr, S. McDonagh, L. Pereira, A. Sali, S.J. Fisher. "Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term." Endocrinology 148, 1059-1079, 2007.

189.

2007

C.V. Robinson, A. Sali, W. Baumeister. "The molecular sociology of the cell." Nature 450, 973-982, 2007.

190.

2007

F. Alber, S. Dokudovskaya, L.M. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, B.T. Chait, A. Sali, M.P. Rout. "The molecular architecture of the nuclear pore complex." Nature 450, 695-701, 2007.

191.

2007

F. Alber, S. Dokudovskaya, L.M. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, B.T. Chait, M.P. Rout, A. Sali. "Determining the architectures of macromolecular assemblies." Nature 450, 683-694, 2007.

192.

2008

N. Eswar, D. Eramian, B. Webb, M.Y. Shen, A. Sali. "Protein structure modeling with MODELLER." Methods Mol Biol 426, 145-159, 2008.

193.

2008

T. Schwede, A. Sali, N. Eswar, M.C. Peitsch. "Protein Structure Modeling." In: Computational Structural Biology. Ed: T. Schwede, M.C. Peitsch, pp. 3-35, World Scientific Publishing Ltd., Singapore, 2008.

194.

2008

Y. Cong, M. Topf, A. Sali, P. Matsudaira, M. Dougherty, W. Chiu, M.F. Schmid. "Crystallographic conformers of actin in a biologically active bundle of filaments." J Mol Biol 375, 331-336, 2008.

195.

2008

C.R. Booth, A.S. Meyer, Y. Cong, M. Topf, A. Sali, S.J. Ludtke, W. Chiu, J. Frydman. "Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT." Nat Struct Mol Biol 15, 746-753, 2008.

196.

2008

S.K. Burley, S.C. Almo, J.B. Bonanno, M.R. Chance, S. Emtage, A. Fiser, A. Sali, J.M. Sauder, S. Swaminathan. "Structure Genomics of Protein Superfamilies." In: Structural Bioinformatics, 2nd Edition. Ed: J. Gu, P.E. Bourne, Wiley-Blackwell, New York, NY, 2008.

197.

2008

F. Alber, B.T. Chait, M.P. Rout, A. Sali. "Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints." In: Protein-protein interactions and networks: identification, characterization and prediction. Ed: A. Panchenko, T. Przytycka, pp. 99-114, Springer-Verlag, London, UK, 2008.

198.

2008

P. Chandramouli, M. Topf, J.F. Menetret, N. Eswar, J.J. Cannone, R.R. Gutell, A. Sali, C.W. Akey. "Structure of the mammalian 80S ribosome at 8.7 A resolution." Structure 16, 535-548, 2008.

199.

2008

F. Alber, F. Forster, D. Korkin, M. Topf, A. Sali. "Integrating diverse data for structure determination of macromolecular assemblies." Annu Rev Biochem 77, 443-477, 2008.

200.

2008

M. Topf, K. Lasker, B. Webb, H. Wolfson, W. Chiu, A. Sali. "Protein structure fitting and refinement guided by cryo-EM density." Structure 16, 295-307, 2008.

201.

2008

J. Espadaler, N. Eswar, E. Querol, F.X. Aviles, A. Sali, M.A. Marti-Renom, B. Oliva. "Prediction of enzyme function by combining sequence similarity and protein interactions." BMC Bioinformatics 9, 249, 2008.

202.

2008

F. Aguero, B. Al-Lazikani, M. Aslett, M. Berriman, F.S. Buckner, R.K. Campbell, S. Carmona, I.M. Carruthers, A.W. Chan, F. Chen, G.J. Crowther, M.A. Doyle, C. Hertz-Fowler, A.L. Hopkins, G. McAllister, S. Nwaka, J.P. Overington, A. Pain, G.V. Paolini, U. Pieper, S.A. Ralph, A. Riechers, D.S. Roos, A. Sali, D. Shanmugam, T. Suzuki, W.C. Van Voorhis, C.L. Verlinde. "Genomic-scale prioritization of drug targets: the TDR Targets database." Nat Rev Drug Discov 7, 900-907, 2008.

203.

2008

R. Karchin, M. Agarwal, A. Sali, F. Couch, M.S. Beattie. "Classifying Variants of Undetermined Significance in BRCA2 with Protein Likelihood Ratios." Cancer Inform 6, 203-216, 2008.

204.

2008

K.A. Krukenberg, F. Forster, L.M. Rice, A. Sali, D.A. Agard. "Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90." Structure 16, 755-765, 2008.

205.

2008

D. Eramian, N. Eswar, M.Y. Shen, A. Sali. "How well can the accuracy of comparative protein structure models be predicted?" Protein Sci 17, 1881-1893, 2008.

206.

2008

F. Forster, B. Webb, K.A. Krukenberg, H. Tsuruta, D.A. Agard, A. Sali. "Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies." J Mol Biol 382, 1089-1106, 2008.

207.

2008

C.M. Anderson, D. Korkin, D.L. Smith, S. Makovets, J.J. Seidel, A. Sali, E.H. Blackburn. "Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break." Genes Dev 22, 854-859, 2008.

208.

2008

R.A. Chiang, A. Sali, P.C. Babbitt. "Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies." PLoS Comput Biol 4, e1000142, 2008.

209.

2008

S. Mahrus, J.C. Trinidad, D.T. Barkan, A. Sali, A.L. Burlingame, J.A. Wells. "Global Sequencing of Proteolytic Cleavage Sites in Apoptosis by Specific Labeling of Protein N Termini." Cell 134, 866-876, 2008.

210.

2008

I.I. Serysheva, S.J. Ludtke, M.L. Baker, Y. Cong, M. Topf, D. Eramian, A. Sali, S.L. Hamilton, W. Chiu. "Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel." Proc Natl Acad Sci U S A 105, 9610-9615, 2008.

211.

2008

S. Graslund, P. Nordlund, J. Weigelt, B.M. Hallberg, J. Bray, O. Gileadi, S. Knapp, U. Oppermann, C. Arrowsmith, R. Hui, J. Ming, S. dhe-Paganon, H. Park, A. Savchenko, A. Yee, A. Edwards, R. Vincentelli, C. Cambillau, R. Kim, S. Kim, Z. Rao, Y. Shi, T.C. Terwilliger, C. Kim, L. Hung, G.S. Waldo, Y. Peleg, S. Albeck, T. Unger, O. Dym, J. Prilusky, J.L. Sussman, R.C. Stevens, S.A. Lesley, I.A. Wilson, A. Joachimiak, F. Collart, I. Dementieva, M.I. Donnelly, W.H. Eschenfeldt, Y. Kim, L. Stols, R. Wu, M. Zhou, S.K. Burley, J.S. Emtage, J.M. Sauder, D. Thompson, K. Bain, J. Luz, T. Gheyi, F. Zhang, S. Atwell, S.C. Almo, J.B. Bonanno, A. Fiser, S. Swaminathan, F.W. Studier, M.R. Chance, A. Sali, T.B. Acton, R. Xiao, L. Zhao, L.C. Ma, J.F. Hunt, L. Tong, K. Cunningham, M. Inouye, S. Anderson, H. Janjua, R. Shastry, C.K. Ho, D. Wang, H. Wang, M. Jiang, G.T. Montelione, D.I. Stuart, R.J. Owens, S. Daenke, A. Schutz, U. Heinemann, S. Yokoyama, K. Bussow, K.C. Gunsalus. "Protein production and purification (vol 5, pg 135, 2008)." Nat Methods 5, 369-369, 2008.

212.

2009

N. Eswar, A. Sali. "Protein Structure Modeling." In: From Molecules to Medicine, Structure of Biological Macromolecules and Its Relevance in Combating New Diseases and Bioterrorism. Ed: J.L. Sussman, P. Spadon, pp. 139-151, Springer-Verlag, Dordrecht, The Netherlands, 2009.

213.

2009

U. Pieper, R. Chiang, J.J. Seffernick, S.D. Brown, M.E. Glasner, L. Kelly, N. Eswar, J.M. Sauder, J.B. Bonanno, S. Swaminathan, S.K. Burley, X. Zheng, M.R. Chance, S.C. Almo, J.A. Gerlt, F.M. Raushel, M.P. Jacobson, P.C. Babbitt, A. Sali. "Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies." J Struct Funct Genom 10, 107-125, 2009.

214.

2009

U. Pieper, N. Eswar, B.M. Webb, D. Eramian, L. Kelly, D.T. Barkan, H. Carter, P. Mankoo, R. Karchin, M.A. Marti-Renom, F.P. Davis, A. Sali. "MODBASE, a database of annotated comparative protein structure models and associated resources." Nucleic Acids Res 37, D347-354, 2009.

215.

2009

F.A. Hays, Z. Roe-Zurz, M. Li, L. Kelly, F. Gruswitz, A. Sali, R.M. Stroud. "Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination." J Struct Funct Genom 10, 9-16, 2009.

216.

2009

M. Li, F.A. Hays, Z. Roe-Zurz, L. Vuong, L. Kelly, C.M. Ho, R.M. Robbins, U. Pieper, J.D. O'Connell 3rd, L.J. Miercke, K.M. Giacomini, A. Sali, R.M. Stroud. "Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening." J Mol Biol 385, 820-830, 2009.

217.

2009

M.E. Peterson, F. Chen, J.G. Saven, D.S. Roos, P.C. Babbitt, A. Sali. "Evolutionary constraints on structural similarity in orthologs and paralogs." Protein Sci 18, 1306-1315, 2009.

218.

2009

D. Russel, K. Lasker, J. Phillips, D. Schneidman-Duhovny, J.A. Velazquez-Muriel, A. Sali. "The structural dynamics of macromolecular processes." Curr Opin Cell Biol 21, 97-108, 2009.

219.

2009

T. Schwede, A. Sali, B. Honig, M. Levitt, H.M. Berman, D. Jones, S.E. Brenner, S.K. Burley, R. Das, N.V. Dokholyan, R.L. Dunbrack Jr, K. Fidelis, A. Fiser, A. Godzik, Y.J. Huang, C. Humblet, M.P. Jacobson, A. Joachimiak, S.R. Krystek Jr, T. Kortemme, A. Kryshtafovych, G.T. Montelione, J. Moult, D. Murray, R. Sanchez, T.R. Sosnick, D.M. Standley, T. Stouch, S. Vajda, M. Vasquez, J.D. Westbrook, I.A. Wilson. "Outcome of a workshop on applications of protein models in biomedical research." Structure 17, 151-159, 2009.

220.

2009

L. Orti, R.J. Carbajo, U. Pieper, N. Eswar, S.M. Maurer, A.K. Rai, G. Taylor, M.H. Todd, A. Pineda-Lucena, A. Sali, M.A. Marti-Renom. "A kernel for open source drug discovery in tropical diseases." PLoS Negl Trop Dis 3, e418, 2009.

221.

2009

K.C. Pandey, D.T. Barkan, A. Sali, P.J. Rosenthal. "Regulatory elements within the prodomain of falcipain-2, a cysteine protease of the malaria parasite Plasmodium falciparum." PLoS One 4(5):e5694, 2009.

222.

2007

R.M. Stroud, S. Choe, J. Holton, H.R. Kaback, W. Kwiatkowski, D.L. Minor, R. Riek, A. Sali, H. Stahlberg, W. Harries. "2007 Annual progress report synopsis of the Center for Structures of Membrane Proteins." J Struct Funct Genom 10, 193-208, 2009.

223.

2009

L. Orti, R.J. Carbajo, U. Pieper, N. Eswar, S.M. Maurer, A.K. Rai, G. Taylor, M.H. Todd, A. Pineda-Lucena, A. Sali, M.A. Marti-Renom. "A kernel for the Tropical Disease Initiative." Nat Biotechnol 27, 320-321, 2009.

224.

2009

O. Fornes, R. Aragues, J. Espadaler, M.A. Marti-Renom, A. Sali, B. Oliva. "ModLink+: Improving fold recognition by using protein-protein interactions." Bioinformatics 25, 1506-1512, 2009.

225.

2009

S. Nickell, F. Beck, S.H.W. Scheres, A. Korinek, F. Forster, K. Lasker, O. Mihalache, N. Sun, I. Nagy, A. Sali, J. Plitzko, J.-M. Carazo, M. Mann, W. Baumeister. "Insights into the Molecular Architecture of the 26S Proteasome." Proc Natl Acad Sci U S A 29, 11943-11947, 2009.

226.

2009

K. Lasker, M. Topf, A. Sali, H.J. Wolfson. "Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly." J Mol Biol 388, 180-194, 2009.

227.

2009

M.S. Madhusudhan, B.M. Webb, M.A. Marti-Renom, N. Eswar, A. Sali. "Alignment of multiple protein structures based on sequence and structure features." Protein Eng Des Sel 22, 569-574, 2009.

228.

2009

J.A. DeGrasse, K.N. DuBois, D. Devos, T.N. Siegel, A. Sali, M.C. Field, M.P. Rout, B.T. Chait. "The Establishment of Nuclear Pore Complex Architecture Occurred Early in Evolution." Mol Cell Proteomics 8, 2119-2130, 2009.

229.

2009

L. Kelly, U. Pieper, N. Eswar, F.A. Hays, M. Li, Z. Roe-Zurz, D. Kroetz, K.M. Giacomini, R.M. Stroud, A. Sali. "A survey of integral alpha-helical membrane proteins." J Struct Funct Genomics 10, 269-280, 2009.

230.

2009

T. Lezon, A. Sali, I. Bahar. "Global motions of the nuclear pore complex:Insights from Elastic Network Models." PLoS Comp Biol 5, e1000496, 2009.

231.

2009

D.J. Taylor, B. Devkota, A.D. Huang, M. Topf, N. Eswar, A. Sali, S.C. Harvey, J. Frank. "Comprehensive Molecular Structure of the Eukaryotic Ribosome." Structure 17, 1591-1604, 2009.

232.

2009

H. Fan, J.J. Irwin, B.M. Webb, G. Klebe, B. Shoichet, A. Sali. "Molecular Docking Screens Using Comparative Models of Proteins." J Chem Inf Model 49, 2512-2527, 2009.

233.

2009

F. Forster, K. Lasker, F. Beck, S. Nickell, A. Sali, W. Baumeister. "An Atomic Model AAA-ATPase/20S core particle sub-complex of the 26S proteasome." Biochem Biophys Res Commun 388, 228-233, 2009.

234.

2009

D. Kroetz, N. Ahituv, E. Burchard, S. Guo, A. Sali, K. Giacomini. "The Pharmacogenomics Center of the University of California, Sam Francisco: At the interface of genomics, biological mechanism and drug therapy." Pharmacogenomics 10, 1569-1576, 2009.

235.

2010

F.P. Davis, A. Sali. "The overlap of small molecule and protein binding sites within families of protein structures." PLoS Comp Biol 6, e1000668, 2010.

236.

2010

D. Barkan, D. Hostetter, S. Mahrus, U. Pieper, J. Wells, C. Craik, A. Sali. "Prediction of Protease Substrates using Sequence and Structure Features." Bioinformatics 26, 1714-1722, 2010.

237.

2010

F. Gruswitz, S. Chaudhary, J. Ho, A. Schlessinger, P. Bobak, C. Ho, A. Sali, C. Westhoff, R. Stroud. "Function of Human Rh based on Structure of RhCG at 2.1 Å." Proc Natl Acad Sci U S A 107, 9638-9643, 2010.

238.

2010

L. Chen, B. Pawlikowski, A. Schlessinger, S. More, D. Stryke, S.J. Johns, M. Portman, T.E. Ferrin, A. Sali, K. Giacomini. "Role of organic cation transporter 3 (SLC22A3) and Its missense variants in the pharmacologic action of metformin." Pharmacogenet Genomics 20, 687-699, 2010.

239.

2010

A. Schlessinger, P. Matsson, J.E. Shima, U. Pieper, S.W. Yee, L. Kelly, L. Apeltsin, R.M. Stroud, T.E. Ferrin, K.M. Giacomini, A. Sali. "Comparison of Human Solute Carriers." Protein Sci 19, 412-428, 2010.

240.

2010

D. Schneidman-Duhovny, M. Hammel, A. Sali. "FoXS: A Web Server for Rapid Computation and Fitting of SAXS Profiles." Nucleic Acids Res 38, 541-544, 2010.

241.

2010

K. Lasker, J.L. Phillips, D. Russel, J. Velazquez-Muriel, D. Schneidman-Duhovny, B. Webb, A. Schlessinger, A. Sali. "Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data." Mol Cell Proteomics 9, 1689-1702, 2010.

242.

1992

P. Sampathkumar, S.A. Ozyurt, J. Do, K.T. Bain, M. Dickey, L.A. Rodgers, T. Gheyi, A. Sali, S.J. Kim, J. Phillips, U. Pieper, J. Fernandez-Martinez, J.D. Franke, A. Martel, H. Tsuruta, S. Atwell, D.A. Thompson, J.S. Emtage, S.R. Wasserman, M.P. Rout, J.M. Sauder, S.K. Burley. "Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup 145." Proteins:Struct Funct Bioinform 78, 1992-1998, 2010.

243.

2010

P. Sampathkumar, F. Lu, X. Zhao, Z. Li, J. Gilmore, K. Bain, M.E. Rutter, T. Gheyi, K. Schwinn, J. Bonanno, U. Pieper, J.E. Fajardo, A. Fiser, S. Almo, A. Swaminathan, M. Chance, D. Baker, S. Atwell, D. Thompson, J.S. Emtage, S. Wasserman, A. Sali, J.M. Sauder, S. Burley. "Structure of a putative BenF-like porin from Pseudomanas fluorescens Pf-5 at 2.6 Å resolution." Proteins:Struct Funct Bioinform 78, 3056-3062, 2010.

244.

2010

K. Lasker, A. Sali, H.J. Wolfson. "Determining macromolecular assembly structures by molecular docking and fitting into an electron density map." Proteins:Struct Funct Bioinform 78, 3205-3211, 2010.

245.

2010

L. Chen, M. Takizawa, E. Chen, A. Schlessinger, J.H. Choi, J. Segenthelar, A. Sali, M. Kubo, S. Nakamura, Y. Iwamoto, N. Iwasaki, K.M. Giacomini. "Genetic polymorphisms in the organic cation transporter 1, OCT1, in Chinese and Japanese populations, exhibit altered function." J Pharmacol Exp Ther 1, 42-50, 2010.

246.

2010

L. Kelly, H. Fukushima, R. Karchin, J.M. Gow, L.W. Chinn, U. Pieper, M.R. Segal, D.L. Kroetz, A. Sali. "Functional Hot Spots in Human ATP-binding Cassette Transporter Nucleotide Binding Domains." Protein Sci 19, 2110-2121, 2010.

247.

2010

F. Forster, K. Lasker, S. Nickell, A. Sali, W. Baumeister. "Toward an integrated structural model of the 26S proteasome." Mol Cell Proteomics 9, 1666-1677, 2010.

248.

2011

D. Schneidman-Duhovny, M. Hammel, A. Sali. "Macromolecular docking restrained by a small angle X-ray scattering profile." J Struct Biol 3, 461-471, 2011.

249.

2011

L. Kelly, H. Fukushima, R. Karchin, J.M. Gow, L.W. Chinn, U. Pieper, M.R. Segal, D.L. Kroetz, A. Sali. "Response to "Predictable difficulty or difficulty to predict" by Tamas Aranyi, Krisztina Fulop, Orsolya Symmons, Viola Pomozi, and Andras Varadi." Protein Sci 20, 4-5, 2011.

250.

2011

U. Pieper, B.M. Webb, D.T. Barkan, D. Schneidman-Duhovny, A. Schlessinger, H. Braberg, Z. Yang, E.C. Meng, E.F. Pettersen, C.C. Huang, R.S. Datta, P. Sampathkumar, M.S. Madhusudhan, K. Sjolander, T.E. Ferrin, S.K. Burley, A. Sali. "ModBase, a database of annotated comparative protein structure models, and associated resources." Nucleic Acids Res 39, 465-474, 2011.

251.

2011

S.S. Kamat, A. Bagaria, D. Kumaran, G.P. Holmes-Hampton, H. Fan, A. Sali, J.M. Sauder, S.K. Burley, P.A. Lindahl, S. Swaminathan, F.M. Raushel. "Catalytic Mechanism and Three-Dimensional Structure of Adenine Deaminase." Biochemistry (Mosc) 50, 1917-1927, 2011.

252.

2011

B. Webb, K. Lasker, D. Schneidman-Duhovny, E. Tjioe, J. Phillips, S.J. Kim, J. Velazquez-Muriel, D. Russel, A. Sali. "Modeling of Proteins and their Assemblies with the Integrative Modeling Platform." In: Methods in Molecular Biology, pp. 377-397, Humana Press, 2011.

253.

2011

P. Sampathkumar, T. Gheyi, S.A. Miller, K.T. Bain, M. Dickey, J.B. Bonanno, Kim. S.J., J. Phillips, U. Pieper, J. Fernandez-Martinez, J. Franke, A. Martel, H. Tsuruta, S. Atwell, D.A. Thompson, J.S. Emtage, S.R. Wasserman, M.P. Rout, A. Sali, J.M. Sauder, S.K. Burley. "Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the Nuclear Pore Complex." Proteins:Struct Funct Bioinform 79, 1672-1677, 2011.

254.

2011

S.S. Kamat, H. Fan, J.M. Sauder, S.K. Burley, B.K. Shoichet, A. Sali, F.M. Raushel. "Enzymatic deamination of the epigenetic base N-6-methyladenine." J Am Chem Soc 133, 2080-2083, 2011.

255.

2011

S. Dokudovskaya, F. Waharte, A. Schlessinger, U. Pieper, D.P. Devos, I.M. Cristea, R. Williams, J. Salamero, B.T. Chait, A. Sali, M.C. Field, M.C. Rout, C. Dargemont. "A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae." Mol Cell Proteomics, M110.006478, 2011.

256.

2011

M. Field, A. Sali, M. Rout. "On a bender: Bars, ESCRTs, COPs, and finally getting your coat." J Cell Biol 193, 963-972, 2011.

257.

2011

H. Fan, D. Schneidman, J.J. Irwin, G. Dong, B. Shoichet, A. Sali. "Statistical Potential for Modeling and Ranking Protein-Ligand Interactions." J Chem Inf Model 51, 3078-3092, 2011.

258.

2011

S. Jager, P. Cimermancic, N. Gulbahce, J. Johnson, K. McGovern, S. Clarke, M. Shales, G. Mercenne, K. Li, H. Barry, G. Jang, E. Akiva, L. Pache, J. Marlett, S. Roth, M. Stephens, I. D'Orso, J. Fernandes, M. Fahey, C. Mahon, A. O'Donoghue, A. Todorovic, J. Morris, D. Maltby, T. Alber, G. Cagney, F. Bushman, J. Young, S. Chanda, W. Sundquist, T. Kortemme, R. Hernandez, C. Craik, A. Burlingame, A. Sali, A. Frankel, N. Krogan. "Global Landscape of HIV-Human Protein Complexes." Nature 481, 365-370, 2011.

259.

2011

S. Jager, D.Y. Kim, K. Shindo, E. Kwon, R. LaRue, C. Mahon, P. Cimermancic, L. Yen, D. Stanley, M. Li, A. Burlingame, A. Sali, C. Craik, R. Harris, J. Gross, N. Krogan. "Vif Hijacks CBFβ to Degrade APOBEC3G and Promote HIV-1 Infection." Nature 481, 371-375, 2011

260.

2011

E. Tjioe, K. Lasker, B. Webb, H. Wolfson, A. Sali. "MultiFit: A web server for fitting multiple protein structures into their electron microscopy density map." Nucleic Acids Res 39, 167-170, 2011.

261.

2011

J. Carlsson, R. Coleman, V. Setola, J. Irwin, H. Fan, A. Schlessinger, A. Sali, B. Roth, B. Shoichet. "Structure-based Ligand Discovery Against a Homology Model and X-ray Structure of the Dopamine D3 Receptor." Nat Chem Biol 7, 769-778, 2011.

262.

2011

A. Schlessinger, E. Geier, H. Fan, J. Irwin, B. Shoichet, K. Giacomini, A. Sali. "Structure-based Discovery of Prescription Drugs that Interact with the Norepinephrine Transporter, NET." Proc Natl Acad Sci USA 108, 15810-15815, 2011.

263.

2011

263. J. Choi, S. Yee, A. Ramirez, K. Morrissey, G. Jang, P. Joski, J. Mefford, S. Hesselson, A. Schlessinger, G. Jenkins, R. Castro, S. Johns, D. Stryke, A. Sali, T. Ferrin, J. Witte, P. Kwok, D. Roden, R. Wilke, C. McCarty, R. Davis, K. Giacomini. "A Common Promoter Variant in MATE2-K Is Associated with Poor Response to Metformin." Clin Pharmacol Ther 90, 674-684, 2011.

264.

2011

Z. Yang, K. Lasker, D. Schneidman-Duhovny, B. Webb, C. Huang, E. Pettersen, T. Goddard, E. Meng, A. Sali, T. Ferrin. "UCSF Chimera, MODELLER, and IMP: an integrated Modeling System." J Struct Biol 179, 269-278, 2011.

265.

2011

265. A.M. Goble, H. Fan, A. Sali, F.M. Raushel. "Discovery of a Cytokinin Deaminase." ACS Chem Biol 6, 1036-1040, 2011.

266.

2011

J. Gerlt, K. Allen, S. Almo, R. Armstrong, P. Babbitt, J. Cronan, D. Dunaway-Mariano, H. Imker, M. Jacobson, W. Minor, C. Poulter, F. Raushel, A. Sali, B. Shoichet, J. Sweedler. "The Enzyme Function Initiative." Biochemistry 50, 9950-9962, 2011

267.

2011

K. Lasker, J. Velazquez-Muriel, B. Webb, Z. Yang, T.E. Ferrin, A. Sali. "Macromolecular assembly structures by comparative modeling and electron microscopy." In: Methods in Molecular Biology. Ed: J. Walker, Humana Press, New York, NY, 2011.

268.

2012

H. Fan, J. Irwin, A. Sali. "Virtual Ligand Screening Against Comparative Protein Structure Models." Methods Mol Biol 819, 105-126, 2012.

269.

2012

J. Fernandez-Martinez, J. Phillips, M. Sekedat, R. Diaz-Avalos, J. Velazquez-Muriel, J. Franke, R. Williams, D. Stokes, B. Chait, A. Sali, M. Rout. "Structure-function Map for a Heptameric Component of the Nuclear Pore Complex." J Cell Biol 196, 419-434, 2012.

270.

2012

R. Henderson, A. Sali, H. Berman, W. Chiu, G. Kleyweft, C. Lawson, M. Baker, B. Carragher, B. Devkota, K. Downing, E. Egelman, Z. Feng, J. Frank, N. Grigorieff, W. Jiang, S. Ludtke, O. Medalia, P. Penczek, P. Rosenthal, M. Rossmann, M. Schmid, G. Schroder, A. Steven, D. Stokes, J. Westbrook, W. Wriggers, H. Yang, J. Young. "Outcome of the First Electron Microscopy Validation Task Force Meeting." Structure 20, 205-214, 2012.

271.

2012

P. Weinkam, J. Pons, A. Sali. "Structure-based Model of Allostery Predicts Coupling Between Distant Sites." Proc Natl Acad Sci USA 109, 4875-4880, 2012.

272.

2012

D. Russel, K. Lasker, B. Webb, J. Velazquez-Muriel, E. Tjioe, D. Schneidman-Duhovny, B. Peterson, A. Sali. "Putting the pieces together: integrative structure determination of macromolecular assemblies." PLoS Biol 10, e1001244, 2012.

273.

2012

G. Pathare, I. Nagy, S. Bohn, P. Unverdorben, A. Hubert, R. Korner, S. Nickell, K. Lasker, A. Sali, T. Tamura, T. Nishioka, F. Forster, W. Baumeister, A. Bracher. "The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together." Proc Natl Acad Sci USA 109, 149-154, 2012.

274.

2012

K. Lasker, F. Forster, S. Bohn, T. Walzthoeni, E. Villa, P. Unverdorben, F. Beck, R. Aebersold, A. Sali, W. Baumeister. "Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach." Proc Natl Acad Sci USA 109, 1380-1387, 2012.

275.

2012

P. Sampathkumar, S.J. Kim, D. Manglicmot, K.T. Bain, J. Gilmore, T. Gheyi, J. Phillips, U. Pieper, J. Fernandez-Martinez, J. Franke, T. Matsui, H. Tsuruta, S. Atwell, D. Thompson, J.S. Emtage, S. Wasserman, M. Rout, A. Sali, J.M. Sauder, S.C. Almo, S.K. Burley. "Atomic structure of the Nuclear Pore Complex targeting domain of Nup116 homologue from the yeast, Candida glabrata." Proteins:Struct Funct Bioinform 8, 2110-2116, 2012.

276.

2012

C. Klammt, I. Maslennikov, M. Bayrhuber, C. Eichmann, N. Vajpai, E. Chiu, K. Blain, L. Esquivies, H. Kwon, B. Balana, U. Pieper, A. Sali, P. Slesinger, W. Kwiatkowski, R. Rick, S. Choe. "Facile Backbone structure determination of human membrane proteins by NMR spectroscopy." Nat Methods 8, 834-839, 2012.

277.

2012

D. Schneidman-Duhovny, A. Rossi, A. Avila-Sakar, S.J. Kim, J. Velazquez-Muriel, P. Strop, H. Liang, K.A. Krukenberg, M. Liao, H.M. Kim, S. Sobhanifar, V. Dotsch, A. Raipal, J. Pons, D.A. Agard, Y. Cheng, A. Sali. "A Method for Integrative Structure Determination of Protein-Protein Complexes." Bioinformatics 28, 3282-3289, 2012.

278.

2012

V. Puizdar, T. Zajc, E. Zerovnik, M. Renko, U. Pieper, N. Eswar, A. Sali, I. Dolenc, V. Turk. "Biochemical Characterization and Structural Modeling of Human Cathepsin E Variant 2 in Comparison to the Wild-type Protein." Biol Chem 393, 177-186, 2012.

279.

2012

A. Morin, J. Urban, P.D. Adams, I. Foster, A. Sali, D. Baker, P. Sliz. "Shining Light into Black Boxes." Science 336, 159-160, 2012.

280.

2012

H. Braberg, B. Webb, E. Tjioe, U. Pieper, A. Sali, M.S. Madhusudhan. "SALIGN: A webserver for alignment of multiple protein sequences and structures." Bioinformatics 15, 2072-2073, 2012.

281.

2012

J.A. Horst, U. Pieper, A. Sali, L. Zhan, G. Chopra, R. Samudrala, J.D.B. Featherstone. "Strategic protein target analysis for developing drugs to stop dental caries." Adv Dent Res 22, 86-93, 2012.

282.

2012

J. Trinidad, D. Barkan, B. Gulledge, A. Thalhammer, A. Sali, R. Schoepfer, A. Burlingame. "Global Identification and Characterization of Both O-GlcNAcylation and Phosphorylation at the Murine Synapse." Mol Cell Proteomics 11, 215-229, 2012.

283.

2012

O. Martinez-Avila, S. Wu, S.J. Kim, Y. Cheng, F. Khan, R. Samudrala, A. Sali, J. Horst, S. Habelitz. "Self-assembly of Filamentous Amelogenin Requires Calcium and Phosphate: From Dimers via Nanoribbons to Fibrils." Biomacromolecules 13, 3494-3502, 2012.

284.

2012

J.A. Velazquez-Muriel, K. Lasker, D. Russel, J. Phillips, B. Webb, D. Schneidman-Duhovny, A. Sali. "Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images." Proc Natl Acad Sci USA 109, 18821-18826, 2012.

285.

2012

P. Kolb, K. Phan, Z. Gao, A. Marko, A. Sali, K.A. Jacobson. "Limits of ligand selectivity from docking to models: In silico screening for A1 adenosine receptor antagonists." PLoS One 7, e49910, 2012.

286.

2012

A. Schlessinger, M.B. Wittwer, A. Dahlin, N. Khuri, M. Bonomi, H. Fan, K. Giacomini, A. Sali. "High Selectivity of the γ-Aminobutyric Acid Transporter 2 (GAT-2, SLC6A13) Revealed by Structure-based Approach." J Biol Chem 287, 37745-37756, 2012.

287.

2012

D. Schneidman-Duhovny, S.J. Kim, A. Sali. "Integrative structural modeling with small angle X-ray scattering profiles." BMC Struct Biol 12, 17, 2012.

288.

2012

Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski M, Case D, Chazin W, Cross T, Dames S, Kessler H, Lange O, Madl T, Reif B, Sattler M, Eliezer D, Fersht A, Forman-Kay J, Kay L, Fraser J, Gross J, Kortemme T, Sali A, Fujiwara T, Gardner K, Luo X, Rizo-Rey J, Rosen M, Gil R, HO C, Rule G, Gronenborn A, Ishima R, Klein-Seetharaman J, Tang P, van der Wel P, Xu Y, Grzesiek S, Hiller S, Seelig J, Laue E, Mott H, Nietlispach D, Barsukiv I, Lian L, Middleton D, Blumenschein T, Moore G, Campbell I, Schnell J, Vakonakis I, Watts A, Conte M, Mason J, Pfuhl M, Sanderson M, Craven J, Williamson M, Dominguez C, Roberts G, Gunther U, Overduin M, Werner J, Williamson P, Blindauer C, Crump M, Driscoll P, Frenkiel T, Golovanov A, Matthews S, Parkinson J, Uhrin D, Williams M, Neuhaus D, Oschkinat H, Ramos A, Shaw D, Steinbeck C, Vendruscolo M, Vuister G, Walters K, Weinstein H, Wuthrich K, Yodoyama S. In support of the BMRB. Nat Struct Mol Biol 19, 854-860, 2012. PMCID TBD by Journal

289.

2013

H. Fan, D. Hitchcock, R. Seidel, B. Hillerich, H. Lin, S. Almo, A. Sali, B. Shoichet, F. Raushel. "The Assignment of Pterin Deaminase Activity to an Enzyme of Unknown Function Guided by Homology Modeling and Docking." J Am Chem Soc 135, 795-803, 2013.

290.

2013

M.B. Wittwer, A.A. Zur, N. Khuri, Y. Kido, A. Kosaka, X. Zhang, K.M. Morrissey, A. Sali, Y. Huang, K.M. Giacomini. "Discovery of potent, selective multidrug and toxin extrusion Transporter 1 (MATE1, SLC47A1) inhibitors through prescription drug profiling and computational modeling." J Med Chem 56, 781-795, 2013.

291.

2013

U. Pieper, A. Schlessinger, E. Kloppmann, G.A. Chang, J.J. Chou, M. Dumont, B. Fox, P. Fromme, W. Hendrickson, M. Malkowski, D. Rees, D. Stokes, M.H.B. Stowell, M. Wiener, B. Rost, R. Stroud, R. Stevens, A. Sali. "Coordinating the impact of structural genomics on the human a-helical transmembrane proteome." Nat Struct Mol Biol 20, 135-138, 2013.

292.

2013

P. Sampathkumar, S.J. Kim, P. Upla, W. Rice, J. Phillips, B. Timney, U. Pieper, J. Bonanno, J. Fernandez-Martinez, Z. Hakhverdyan, N. Ketaren, T. Matsui, R. Weiss, D. Stokes, J.M. Sauder, S. Burley, A. Sali, M. Rout, S. Almo. "Structure, dynamics, evolution and function of a major scaffold component in the Nuclear Pore Complex." Structure 21, 560-571, 2013.

293.

2013

H. Gradisar, S. Bozic, T. Doles, D. Vengust, I. Hafner-Bratkovic, A. Mertelj, B. Webb, A. Sali, S. Klavzar, R. Jerala. "Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments." Nat Chem Biol 9, 362-366, 2013.

294.

2013

B. Pedersen, H. Kumar, A. Waight, A. Risenmay, Z. Roe-Zurz, B. Chau, A. Schlessinger, M. Bonomi, W. Harries, A. Sali, A. Johri, R. Stroud. "Crystal structure of a eukaryotic phosphate transporter." Nature 496, 533-536, 2013.

295.

2013

A. Schlessinger, N. Khuri, K. Giacomini, A. Sali. "Molecular modeling and ligand docking for Solute Carrier (SLC) transporters." Curr Top Med Chem 13, 843-856, 2013.

296.

2013

T. van Dam, M. Townsend, M. Turk, A. Schlessinger, A. Sali, M. Field, M. Huynen. "Evolution of modular intraflagellar transport from a coatomer-like progenitor." Proc Natl Acad Sci USA 110, 6943-6948, 2013.

297.

2013

A. Waight, B. Pedersen, A. Schlessinger, M. Bonomi, B. Chau, Z. Roe-Zurz, A. Risenmay, A. Sali, R. Stroud. "Structural basis for alternating access of a Eukaryotic Calcium/Proton exchanger." Nature 499, 107-110, 2013.

298.

2013

M. Guttman, P. Weinkam, A. Sali, K. Lee. "All-atom ensemble modeling to analyze small angle X-ray scattering of glycosylated proteins." Structure 21, 321-331, 2013.

299.

2013

P. Weinkam, Y.C. Chen, J. Pons, A. Sali. "Impact of mutations on the allosteric conformational equilibrium." J Mol Biol 425, 647-661, 2013.

300.

2013

A. Ward, A. Sali, I. Wilson. "Integrative structural biology." Science 339, 913-915, 2013.

301.

2013

E. Geier, A. Schlessinger, H. Fan, J. Gable, J. Irwin, A. Sali, K. Giacomini. "Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1." Proc Natl Acad Sci USA 110, 5480-5485, 2013.

302.

2013

A. Schlessinger, S.W. Yee, A. Sali, K. Giacomini. "SLC classification: an update." Clin Pharmacol Ther 94, 19-23, 2013.

303.

2013

J. Trewhella, W. Hendrickson, G. Kleywegt, A. Sali, M. Sato, T. Schwede, D. Svergun, J. Tainer, J. Westbrook, H. Berman. "Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB." Structure 21, 875-881, 2013

304.

2013

D. Schneidman-Duhovny, M. Hammel, J. Tainer, A. Sali. "Accurate SAXS profile computation and its assessment by contrast variation experiments." Biophys J 105, 962-974, 2013.

305.

2013

B. Webb, N. Eswar, H. Fan, N. Khuri, U. Pieper, G.Q. Dong, A. Sali. "Comparative Modeling of Drug Target Proteins." In: Chemistry, Molecular Sciences and Chemical Engineering, in press, Elsevier.

306.

2013

D. Hitchcock, H. Fan, J. Kim, M. Vetting, B. Hillerich, R. Seidel, S. Almo, B. Shoichet, A. Sali, F. Raushel. "Structure-guided Discovery of New Deaminase Enzymes." J Am Chem Soc 135, 13927-13933, 2013.

307.

2013

C. Pandya, S. Brown, U. Pieper, A. Sali, D. Dunaway-Mariano, P. Babbitt, Y. Xia, K. Allen. "The consequences of domain insertion on sequence-structure divergence in a superfold." Proc Natl Acad Sci USA 110, 3381-3387, 2013.

308.

2013

P. Weinkam, A. Sali. "Mapping Polymerization and Allostery of Hemoglobin S Using Point Mutations." J Phys Chem B 117, 13058-13068, 2013.

309.

2013

G.Q. Dong, H. Fan, D. Schneidman-Duhovny, B. Webb, A. Sali. "Optimized atomic statistical potentials: Assessment of protein interfaces and loops." Bioinformatics 29, 3158-3166, 2013.

310.

2013

F. Martinez-Jimenez, G. Papadatos, L. Yang, I.M. Wallace, V. Kumar, U. Pieper, A. Sali, J.R. Brown, J.P. Overington, M.A. Marti-Renom. "Target prediction for an open access set of compounds active against Mycobacterium tuberculosis." PLoS Comp Biol, epub ahead of print, 2013.

311.

2013

M. Kostic, C. Lima, A. Sali. "Celebrating 20 Years of Structural Biology." Structure 21, 1477-1478, 2013.

312.

2013

A. Goble, R. Toro, X. Li, A. Ornelas, H. Fan, S. Eswaramoorthy, Y. Patskovsky, B. Hillerich, R. Seidel, A. Sali, B. Shoichet, S. Almo, S. Swaminathan, M. Tanner, F. Raushel. "Deamination of 6-Aminodeoxyfutalosine in Menaquinone Biosynthesis by Distantly Related Enzymes." Biochemistry 52, 6525-6536, 2013.

313.

2013

C. Ryan, P. Cimermancic, Z. Szpiechy, A. Sali, R. Hernandez, N. Krogan. "High-resolution network biology: connecting sequence with function." Nat Rev Genet 14, 865-879, 2013.

314.

2013

K. Berlin, C.A. Castaneda, D. Schneidman-Duhovny, A. Sali, A. Nava-Tudela, D. Fushman. "Recovering a representative conformational ensemble from underdetermined macromolecular structural data." J Am Chem Soc 135, 16595-16609, 2013.

315.

2014

M. Bonomi, E.G. Muller, R. Pellarin, S.J. Kim, D. Russel, R. Ramsden, B.A. Sundin, T.A. Davis, A. Sali. "Determining protein complex structures based on a Bayesian model of in vivo FRET data." Mol Cell Proteomics, epub ahead of print, 2014.

316.

2014

U. Pieper, B. Webb, G.Q. Dong, D. Schneidman-Duhovny, H. Fan, S.J. Kim, N. Khuri, Y. Spill, P. Weinkam, M. Hammel, J. Tainer, M. Nilges, A. Sali. "ModBase, a database of annotated comparative protein structure models, and associated resources." Nucleic Acids Res 42, 336-346, 2014.

317.

2014

K. Molnar, M. Bonomi, R. Pellarin, G. Clinthorne, G. Gonzalez, S. Goldberg, M. Goulian, A. Sali, W. DeGrado. "Cys-Scanning Disulfide Crosslinking and Bayesian Modeling Probe the Transmembrane Signaling Mechanism of the Histidine Kinase, PhoQ." Structure 22, 1239-1251, 2014.

318.

2014

B. Webb, K. Lasker, J. Velazquez-Muriel, D. Schneidman-Duhovny, R. Pellarin, M. Bonomi, C. Greenberg, B. Raveh, E. Tjioe, D. Russel, A. Sali. "Modeling of proteins and their assemblies with the Integrative Modeling Platform." In: Structural Genomics. Ed: Y. Chen, pp. 277-295, Humana Press, London, UK, 2014.

319.

2014

Y. Spill, S.J. Kim, D. Schneidman-Duhovny, D. Russel, B. Webb, A. Sali, M. Nilges. "SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes." J Synchrotron Radiat 21, 203-208, 2014.

320.

2014

J. Johnson, S. Santos, U. Pieper, A. Sali, N. Krogan, P. Beltrao. "Conservation and structural analysis of the Xenopus laevis phospho-proteome." submitted.

321.

2014

G.Q. Dong, S. Calhoun, H. Fan, C. Kalyanaraman, N. London, M. Branch, S. Mashiyama, M. Jacobson, B. Shoichet, P. Babbitt, R. Armstrong, A. Sali. "Prediction of substrates for glutathione transferases by covalent docking." J Chem Inf Model 6, 1687-1699, 2014..

322.

2014

R. Algret, J. Fernandez-Martinez, Y. Shi, S.J. Kim, R. Pellarin, P. Cimermancic, E. Cochet, A. Sali, B. Chait, M. Rout, S. Dokudovskaya. "Molecular Architecture and Function of the SEA Complex - a Modulator of the TORC1 Pathway." Mol Cell Proteomics, epub ahead of print, 2014.

323.

2014

T. Street, X. Zeng, R. Pellarin, M. Bonomi, A. Sali, M. Kelly, F. Chu, D. Agard. "Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone." J Mol Biol 12, 2393-2404, 2014.

324.

2014

X. Zeng-Elmore, X. Gao, R. Pellarin, D. Schneidman-Duhovny, X. Zhang, K. Kozacka, Y. Tang, A. Sali, R. Chalkley, R. Cote, F. Chu. "Molecular architecture of photoreceptor phosphodiesterase." J Mol Biol, epub ahead of print, 2014

325.

2014

J. Erzberger, F. Stengel, R. Pellarin, S. Zhang, T. Schaefer, C. Aylett, P. Cimermancic, D. Boehringer, A. Sali, R. Aebersold, N. Ban. "Molecular architecture of the 40S•eIF1•eIF3 translation initiation complex." Cell 158, 1125-1135, 2014.

326.

2014

D. Schneidman-Duhovny, R. Pellarin, A. Sali. "Uncertainty in Integrative Structural Modeling." Curr Opin Struct Biol, 96-104, 2014.

327.

2014

P. Cimermancic, M.H. Medema, J. Claesen, K. Kurita, L. Wieland Brown, K. Mavrommatis, A. Pati, P.A. Godfrey, M. Koehrsen, J. Clardy, B.W. Birren, E. Takano, A. Sali, R.G. Linington, M. Fischbach. "Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters." Cell 158, 412-421, 2014.

328.

2014

M.H. Medema, P. Cimermancic, A. Sali, E. Takano, M. Fischbach. "A systematic computational analysis of biosynthetic gene cluster evolution: Lessons for engineering biosynthesis." submitted.

329.

2014

S.J. Kim, J. Fernandez-Martinez, P. Sampathkumar, A. Martel, T. Matsui, H. Tsuruta, T. Weiss, A. Markina-Inarrairaegui, J. Bonanno, M. Sauder, S. Burley, S. Almo, M. Rout, A. Sali. "Integrative Structure-Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex." Mol Cell Proteomics, epub ahead of print, 2014.

330.

2014

Y. Shi, J. Fernandez-Martinez, E. Tjioe, R. Pellarin, S.J. Kim, R. Williams, D. Schneidman, A. Sali, M. Rout, B. Chait. "Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex." MolCellProteomics, epub ahead of print, 2014.

331.

2015

B. Webb, A. Sali. Comparative Protein Structure Modeling Using Modeller. In: Current Protoc Bioinformatics, 47, pp. 5.6.1-5.6.32, John Wiley and Sons, 2014.

332.

2015

E. Verschueren, J. Von Dollen, P. Cimermancic, N. Gulbahce, A. Sali, N. Krogan. Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. Curr Protoc Bioinformatics 49, 8.19.1-8.19.16, 2015. PMCID4378866

333.

2015

A. Politis, C. Schmidt, E. Tjioe, A. Sandercock, K. Lasker, Y. Gordiyenko, D. Russel, A. Sali, C. Robinson. Topological models of heteromeric protein assemblies from mass spectrometry: Application to the yeast eIF3:eIF5 complex. Chem Biol 22, 117-128, 2015. PMCID4306531

334.

2015

J. Kollman, C. Greenberg, S. Li, M. Moritz, A. Zelter, K. Fong, J. Fernandez, A. Sali, J. Kilmartin, T. Davis, D. Agard. Ring closure activates yeast γTuRC for species-specific microtubule nucleation. Nat Struct Mol Biol 22, 132-137, 2015. PMCID4318760

335.

2015

J. Johnson, S. Santos, U. Pieper, A. Sali, N. Krogan, P. Beltrao. Prediction of functionally important phospho-regulatory events in Xenopus laevis oocytes. PLOS Comp Bio 11, e1004362, 2015. PMCID4552029

336.

2015

A. Sali, H. Berman, T. Schwede, J. Trewhella, G. Kleywegt, S. Burley, J. Markley, H. Nakamura, P. Adams, A. Bonvin, W. Chiu, M. Dal Peraro, F. Di Maio, T. Ferrin, K. Grunewald, A. Gutmanas, R. Henderson, G. Hummer, K. Iwasaki, G. Johnson, C. Lawson, J. Meiler, M. Marti-Renom, G. Montelione, M. Nilges, R. Nussinov, A. Patwardhan, J. Rappsilber, R. Read, H. Saibil, G. Schroder, C. Schwieters, C. Seidel, D. Svergun, M. Topf, E. Ulrich, S. Velanker, J. Westbrook. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure 23, 1156-67, 2015. PMCID4933300

337.

2015

L. Carter, S.J. Kim, D. Schneidman-Duhovny, J. Stoehr, G. Poncet-Montange, T. Weiss, H. Tsuruta, S. Prusiner, A. Sali. Prion protein-antibody complexes characterized by chromatography-coupled small-angle X-ray scattering. Biophys J 109, 793-805, 2015. PMCID4547163

338.

2015

Y. Shi, R. Pellarin, P. Fridy, J. Fernandez-Martinez, M. Thompson, Y. Li, Q.J. Wang, A. Sali, M. Rout, B. Chait. "A strategy for dissecting the architectures of native macromolecular assemblies." Nat Methods 12, 1135-8, 2015.

339.

2015

J. Luo, P. Cimermancic, S. Viswanath, C. Ebmeier, B. Kim, M. Dehecq, V. Raman, C. Greenberg, R. Pellarin, A. Sali, D. Taatjes, S. Hahn, J. Ranish. Architecture of the human and yeast general transcription and DNA repair factor TFIIH. Mol Cell 59, 794-806, 2015. PMCID4560838

340.

2015

P. Robinson, M. Trnka, R. Pellarin, C. Greenberg, D. Bushnell, R. Davis, A. Burlingame, A. Sali, R. Kornberg. Molecular architecture of the yeast Mediator complex. eLife 4, e08719, 2015. PMCID4631838

341.

2015

R. Reid, M. Sgobba, B. Raveh, G. Rastelli, A. Sali, D. Santi. Analytical and simulation-based models for drug release and gel-degradation in a Tetra-PEG hydrogel drug-delivery system. Macromolecules 48, 7359-7369, 2015

342.

2015

C. Smith, K. Lin, A. Stecula, A. Sali, N. Shah. FLT3 D835 mutations confer differential resistance to type II FLT3 inhibitors. Leukemia 29, 2390-2, 2015. PMCID4675689

343.

2015

A.R. Choudhury, E. Sikorska, J. van den Boom, P. Bayer, L. Popenda, K. Szutkowski, S. Jurga, M. Bonomi, A. Sali, I. Zhukov, S. Passamonti, M. Novič. Structural model of the Bilitranslocase transmembrane domain supported by NMR and FRET data. PloS One 10, e0135455, 2015. PMCID4546402

344.

2015

T. Rettenmaier, H. Fan, J. Karpiak, A. Doak, A. Sali, B. Shoichet, J. Wells. Small-molecule allosteric modulators of the protein kinase PDK1 from structure-based docking. J Med Chem 58, 8285-91, 2015

345.

2015

J. LoPiccolo, S.J. Kim, Y. Shi, B. Wu, H. Wu, B.T. Chait, R.H. Singer, A. Sali, M. Brenowitz, A.R. Bresnick, J.M. Backer. Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85α Homodimer. J Biol Chem 290, 30390-405, 2015.

346.

2016

Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. J. Mol. Biol. 428, 709-19, 2016. PMCID4794384

347.

2015

E. Lasater, E. Massi, A. Stecula, J. Politi, S. Tan, C. Smith, M. Gunthorpe, J. Holmes, F. Chehab, A. Sali, N. Shah. Novel TKI-resistant BCR-ABL1 Gatekeeper Residue Mutations Retain in vitro Sensitivity to Axitinib. Leukemia 30, 1405-9, 2016.

348.

2015

D. Schneidman-Duhovny, N. Khuri, G.Q. Dong, M. Winter, E. Shifrut, N. Friedman, C. Craik, P. Paz, F. Aswad, A. Sali. Predicting T-cell epitopes by integrated modeling of APC processing, MHCII presentation, and TCR recognition. Submitted

349.

2016

Sprowl J, Ong SS, Gibson A, Hu S, Du G, Lin W, Li L, Bharill S, Ness R, Stecula A, Offer S, Diasio R, Nies A, Schwab M, Cavaletti G, Schlatter E, Ciarimboli G, Schellens J, Isacoff E, Sali A, Chen T, Baker S, Sparreboom A, Pabla N. A phosphotyrosine switch regulates organic cation transporters. Nat Commun 7, 10880, 2016. PMCID4799362

350.

2016

M.F. Lensink, S. Velankar, A. Kryshtafovych, S. Huang, D. Schneidman-Duhovny, A. Sali, J. Segura, N. Fernandez-Fuentes, S. Viswanath, R. Elber, S. Grudinin, P. Popov, E. Neveu, H. Lee, M. Baek, S. Park, L. Heo, G.R. Lee, C. Seok, S. Qin, H. Zhou, D.W. Ritchie, B. Maigret, M. Devignes, A. Ghoorah, M. Torchala, R.A.G. Chaleil, P.A. Bates, E. Ben-Zeev, M. Eisenstein, S.S. Negi, Z. Weng, T. Vreven, B.G. Pierce, T.M. Borrman, J. Yu, F. Ochsenbein, R. Guerois, A. Vangone, J.P.G.L.M. Rodrigues, G. van Zundert, M. Nellen, L. Xue, E. Karaca, A.S.J. Melquiond, K. Visscher, P.L. Kastritis, A.M.J.J. Bonvin, X. Xu, L. Qiu, C. Yan, J. Li, Z. Ma, J. Cheng, X. Zou, Y. Shen, L.X. Peterson, H. Kim, A. Roy, X. Han, J. Esquivel-Rodriguez, D. Kihara, X. Yu, N.J. Bruce, J.C. Fuller, R.C. Wade, I. Anishchenko, P.J. Kundrotas, I.A. Vakser, K. Imai, K. Yamada, T. Oda, T. Nakamura, K. Tomii, C. Pallara, M. Romero-Durana, B. Jiménez-García, I.H. Moal, J. Férnandez-Recio, J.Y. Joung, J.Y. Kim, K. Joo, J. Lee, D. Kozakov, S. Vajda, S. Mottarella, D.R. Hall, D. Beglov, A. Mamonov, B. Xia, T. Bohnuud, C.A. Del Carpio, E. Ichiishi, N. Marze, D. Kuroda, S.S.R. Burman, J.J. Gray, E. Chermak, L. Cavallo, R. Oliva, A. Tovchigrechko, S.J. Wodak. Prediction of homo- and hetero-protein complexes by ab-initio and template-based docking: a CASP-CAPRI experiment. Proteins, Epub ahead of print. PMCID5030136

351.

2016

B. Raveh, J.M. Karp, S. Sparks, K. Dutta, M.P. Rout, A. Sali, D. Cowburn. Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. Proc Natl Acad Sci USA 113, E2489-97, 2016. PMCID4983827

352.

2016

D. Schneidman, M. Hammel, J. Tainer, A. Sali. FoXS, FoXSDock, and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. Nucleic Acids Res 44, W424-9, 2016. PMCID4987932

353.

2016

Z.A. Chen, R. Pellarin, L. Fischer, A. Sali, M. Nilges, P.N. Barlow, J. Rappsilber. Structure of complement C3(H2O) revealed by quantitative cross-linking/mass spectrometry and modelling. Mol Cell Proteomics 15, 2730-2743, 2016. PMCID4974347

354.

2016

B. Webb, A. Sali. Comparative Protein Structure Modeling Using MODELLER. In: Curr Protoc Protein Sci, 86, pp. 2.9.1-2.9.37, John Wiley and Sons, 2016.

355.

2016

J.C. Watts, K. Giles, D.J. Saltzberg, B.N. Dugger, S. Patel, A. Oehler, S. Bhardwaj, A. Sali, S.B. Prusiner. Guinea Pig Prion Protein Supports Rapid Propagation of Bovine Spongiform Encephalopathy and Variant Creutzfeldt-Jakob Disease Prions. J Virol, in press.

356.

2016

U. Schulze-Gahmen, I. Echeverria, G. Stjepanovic, Y. Bai, H. Lu, D. Schneidman-Duhovny, J.A. Doudna, Q. Zhou, A. Sali, J.H. Hurley. Insights into HIV-1 proviral transcription from the structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex. eLife 5, e15910, 2016.

357.

2016

Timney BL, Raveh B, Mironska R, Trivedi JM, Kim SJ, Russel D, Wente SR, Sali A, Rout MP. Simple rules for passive diffusion through the nuclear pore complex. J Cell Biol. 2016 Oct 10;215(1):57-76. PMID: 27697925

358.

2016

Barkan DT, Cheng X, Celino H, Tran T, Bhandari A, Craik CS, Sali A, Smythe ML. Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23. BMC Bioinformatics 17, 481, 2016. PMCID5120537

359.

2016

Saltzberg DJ, Broughton HB, Pellarin R, Chalmers MJ, Espada A, Dodge JA, Pascal BD, Griffin PR, Humblet C, Sali A. A Residue Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions. J Phys Chem B, in press.

360.

2016

Fernandez-Martinez J, Kim SJ, Shi Y, Upla P, Pellarin R, Gagnon M, Chemmama IE, Wang J, Nudelman I, Zhang W, Williams R, Rice WJ, Stokes DL, Zenklusen D, Chait BT, Sali A, Rout MP. Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform. Cell, in press.

361.

2016

C.H. Greenberg, J. Kollman, A. Zelter, R. Johnson, M.J. MacCoss, T.N. Davis, D.A. Agard, A. Sali. Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure. J Struct Biol 194, 303-10, 2016. PMCID4866596

362.

2016

B. Webb, A. Sali. "Comparative Protein Structure Modeling Using MODELLER." In: Curr Protoc Bioinformatics, 54, pp. 5.6.1-5.6.37, John Wiley and Sons, 2016.

363.

2016

P. Fromme, A. Sali. "Editorial overview: Biophysical and molecular biological methods." Curr Opin Struct Biol 40, ix-xi, 2016.

364.

2016

A. Jahangiri, S.W. Han, M.K. Sidorov, W. Chen, J. Rick, D. Schneidman-Duhovny, S. Mascharak, M. De Lay, J.R. Wagner, B. Imber, P.M. Flanigan, A. Chandra, R. Kuang, B.A. Castro, K. Lu, G. Bergers, A. Sali, W.A. Weiss, M.K. Aghi. Cross-activating c-Met/β1 integrin complex drives metastasis and invasive resistance in cancer. Proc Natl Acad Sci USA 114, E8685-E8694, 2017. PMCID5642678

365.

2017

X. Wang, P. Cimermancic, C. Yu, A. Schweitzer, N. Chopra, J.L. Engel, C. Greenberg, A.S. Huszagh, F. Beck, E. Sakata, Y. Yang, E.J. Novitsky, A. Leitner, P. Nanni, A. Kahraman, X. Guo, J.E. Dixon, S.D. Rychnovsky, R. Aebersold, W. Baumeister, A. Sali, L. Huang. Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome. Mol Cell Proteomics 16, 840-854, 2017. PMCID5417825

366.

2017

N. Khuri, A. Zur, M. Wittwer, L. Lin, S.W. Yee, A. Sali, K. Giacomini. Computational Discovery And Experimental Validation of Inhibitors of the Human Intestinal Transporter, OATP2B1. J Chem Inf Model 57, 1402-1413, 2017.

367.

2017

A. Chen, M. Vieth, D. Timm, C. Humblet, D. Schneidman-Duhovny, I.E. Chemmama, A. Sali, J. Lu, L. Liu. Reconstruction of 3D structures of MET Antibodies from Electron Microscopy 2D Class Averages. PloS One 12, e0175758, 2017. PMCID5391116

368.

2017

E.C. Chen, N. Khuri, X. Liang, A. Stecula, H. Chien, S.W. Yee, Y. Huang, A. Sali, K.M. Giacomini. Discovery of competitive and non-competitive ligands of the organic cation transporter 1 (OCT1; SLC22A1). J Med Chem 60, 2685-2696, 2017.

369.

2017

B. Webb, A. Sali. Protein structure modeling with MODELLER. In: Meth Mol Biol, 1654, pp. 39-54, 2017.

370.

2017

P. Upla, S.J. Kim, P. Sampathkumar, K. Dutta, S.M. Cahill, I.E. Chemmama, R. Williams, J.B. Bonanno, W.J. Rice, D.L. Stokes, D. Cowburn, S.C. Almo, A. Sali, M.P. Rout, J. Fernandez-Martinez. "Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex." Structure, 2017.

371.

2017

P.T. Manna, S. Obado, C. Boehm, C. Gadelha, G. van Miero, A. Sali, B. Chait, M. Rout, M.C. Field. "Lineage-specific proteins essential for endocytosis in trypanosomes." J Cell Sci 130, 1379-1392, 2017.

372.

2017

A. Stecula, A. Schlessinger, K. Giacomini, A. Sali. Human concentrative nucleoside transporter 3 (hCNT3, SLC28A3) forms a cyclic homotrimer. Biochemistry 56, 3475-3483, 2017

373.

2017

C.Y. Zhou, C.I. Stoddard, J.B. Johnston, M.J. Trnka, I. Echeverria, E. Palovcak, A. Sali, A.L. Burlingame, Y. Cheng, G.J. Narlikar. "Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones." Cell Rep 19, 2033-2044, 2017.

374.

2017

S.K. Burley, G. Kurisu, J.L. Markley, H. Nakamura, S. Velankar, H.M. Berman, A. Sali, T. Schwede, J. Trewhella. "PDB-Dev: A Prototype System for Depositing Integrative/Hybrid Structural Models." Structure. 2017 Sep 5;25(9):1317-1318. doi: 10.1016/j.str.2017.08.001. PubMed PMID: 28877501; PubMed Central PMCID:/> PMC5821105.

375.

2017

J. Trewhella, A.P Duff, D. Durand, F. Gabel, J.M. Guss, W.A. Hendrickson, G.L. Hura, D.A. Jacques, N.M. Kriby, A.H. Kwan, J. Perez, L. Pollack, T.M. Ryan, A. Sali, D. Schneidman-Duhovny, T. Schwede, D.I. Svergun, M. Sugiyama, J.A. Tainer, P. Vachette, J. Westbrook, A.E. Whitten. "2017 Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update." Acta Crystallogr D Struct Biol. 2017 Sep 1;73(Pt 9):710-728. doi:/> 10.1107/S2059798317011597. Epub 2017 Aug 18. PubMed PMID: 28876235; PubMed/> Central PMCID: PMC5586245.

376.

2017

S. Viswanath, M. Bonomi, S.J. Kim, V.A. Klenchin, K.C. Taylor, K.C. Yabut, N.T. Umbreit, H.A. Van Epps, J. Meehl, M.H. Jones, D. Russel, J.A. Velazquez-Muriel, M. Winey, I. Rayment, T.N. Davis, A. Sali, E.G. Muller. "The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling." Mol Biol Cell. 2017 Nov 7;28(23):3298-3314. doi: 10.1091/mbc.E17-06-0397. Epub 2017 Aug 16. PubMed PMID: 28814505; PubMed Central PMCID: PMC5687031.

377.

2017

S. Viswanath, I. Chemmama, P. Cimermancic, A. Sali. "Validating Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures." submitted.

378.

2017

M.B. Winter, F. La Greca, S. Arastu-Kapur, P. Cimermancic, T.J. Buchholz, F. Caiazza, J.L. Anderl, M. Ravalin, M.F. Bohn, A. Sali, A.J. O’Donoghue, C.S. Craik. Immunoproteasome Functions Explained by Divergence in Cleavage Specificity and Regulation. eLife 6, e27364, 2017. PMCID5705213

379.

2017

X. Wang, I.E. Chemmama, C. Yu, A. Huszagh, Y. Xu, R. Viner, S.A. Block, P. Cimermancic, S. Rychnovsky, Y. Ye, A. Sali, L. Huang. The proteasome-interacting Ecm29 protein disassembles the 26S proteasome in response to oxidative stress. J Biol Chem 292, 16310-16320, 2017. PMCID5625060

380.

2017

B. Webb, S. Viswanath, M. Bonomi, R. Pellarin, C.H. Greenberg, D. Saltzberg, A. Sali. Integrative structure modeling with the Integrative Modeling Platform. Prot Sci 27, 245-258, 2018. PMCID5734277

381.

2018

T. Yoshizawa, R. Ali, H.Y.J. Fung, K.A. Burke, Y. Lin, S.J. Kim, J. Jiou, M. Soniat, R. Oldenbourg, A. Sali, N.L. Fawzi, M.K. Rosen, Y.M. Chook. Nuclear import receptor inhibits phase separation of FUS through binding to multiple sites. Cell 173, 693-705, 2018.

382.

2018

S. Calhoun, M. Korczynska, D.J. Wichelecki, B. San Francisco, S. Zhao, D.A. Rodionov, M.W. Vetting, N.F. Al-Obaidi, H. Lin, M.J. O’Meara, D.A. Scott, J.H. Morris, D. Russel, S.C. Almo, A.L. Osterman, J.A. Gerlt, M.P. Jacobson, B.K. Shoichet, A. Sali. Prediction of enzymatic pathways by integrative pathway mapping. eLife 7, e31097, 2018. PMCID5788505

383.

2018

A.J. Guy, V. Irani, J.G. Beeson, B. Webb, A. Sali, J.S. Richards, P.A. Ramsland. Proteome-wide mapping of immune features onto Plasmodium protein three-dimensional structures. Sci Rep 8, 4355, 2018. PMCID5847524

384.

2018

S.J. Kim, J. Fernandez-Martinez, I. Nudelman, Y. Shi, W. Zhang, B. Raveh, T. Herricks, B.D. Slaughter, J. Hogan, P. Upla, I.E. Chemmama, R. Pellarin, I. Echeverria, M. Shivaraju, A.S. Chaudhury, J. Wang, R. Williams, J.R. Unruh, C.H. Greenberg, E.Y. Jacobs, Z. Yu, M.J. de la Cruz, R. Mironska, D.L. Stokes, J.D. Aitchison, M.F. Jarrold, J.L. Gerton, S.J. Ludtke, C.W. Akey, B.T. Chait, A. Sali, M.P. Rout. Integrative Structure and Functional Anatomy of a Nuclear Pore Complex. Nature 555, 475-482, 2018.

385.

2018

B. Vallat, B. Webb, J. Westbrook, A. Sali, H.M. Berman. Development of a prototype system for archiving integrative/hybrid structure models of biological macromolecules. Structure, S0969-2126(18)30092-3 [Epub ahead of print], 2018.

386.

2018

J. Singla, K.M. McClary, K.L. White, F. Alber, A. Sali, R.C. Stevens. Opportunities and challenges in building a spatiotemporal multi-scale model of the human pancreatic β-cell. Cell 173, 11-19, 2018.

387.

2018

A. Lyon, A. Zelter, S. Viswanath, A. Maxwell, R. Johnson, K.C.B. Yabut, M. MacCoss, T.N. Davis, E. Muller, A. Sali, D.A. Agard. Spc110 N-Terminal Domains Act Independently to Mediate Stable γ-Tubulin Small Complex Binding and γ-Tubulin Ring Complex Assembly. submitted.

388.

2018

G.L. Holliday, E. Akiva, E.C. Meng, S.D. Brown, S. Calhoun, U. Pieper, A. Sali, S.J. Booker, P.C. Babbitt. Atlas of the Radical SAM Superfamily: Divergent Evolution of Function Using a “Plug & Play” Domain. Methods Enzymol 606, 1-71, 2018

389.

2018

M. Bonomi, S. Hanot, C.H. Greenberg, A. Sali, M. Nilges, M. Vendruscolo, R. Pellarin. Bayesian weighing of electron cryo-microscopy data for integrative structural modeling. Structure, pii: S0969-2126(18)30337-X, 2018.

390.

2018

A. Gaber, S.J. Kim, R.M. Kaake, M. Bencina, N. Krogan, A. Sali, M. Pavsic, B. Lenarcic. EpCAM homo-oligomerization is not the basis for its role in cell-cell adhesion. Sci Rep 8, 13269, 2018

391.

2018

M. Jishage, X. Yu, Y. Shi, S.J. Ganesan, W.Y. Chen, A. Sali, B.T. Chait, F.J. Asturias, R.G. Roeder. Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1. Nat Struct Mol Biol 25, 859-867, 2018

392.

2018

S. Viswanath, A. Sali. Optimizing model representation for integrative structure determination of macromolecular assemblies. Proc Natl Acad Sci USA, pii: 201814649, 2018.

393.

2019

A. Padavannil, P. Sarkar, S.J. Kim, T. Cagatay, J. Jiou, C.A. Brautigam, D.R. Tomchick, A. Sali, S. D'Arcy, Y.M. Chook. Importin-9 wraps around the H2A-H2B core to act as nuclear importer and histone chaperone. eLife 8, e43630, 2019. PMCID6453568

394.

2019

D. Saltzberg, C.H. Greenberg, S. Viswanath, I. Chemmama, B. Webb, R. Pellarin, I. Echeverria, A. Sali. Modeling biological complexes using Integrative Modeling Platform. Methods Mol Biol 2022, 353-377, 2019.

395.

2019

M.P. Rout, A. Sali. Principles for Integrative Structural Biology Studies. Cell 177, 1384-1403, 2019. PMCID6810593

396.

2019

B. Vallat, B. Webb, J. Westbrook, A. Sali, H.M. Berman. Archiving and Disseminating Integrative Structure Models. J Biomol NMR 73, 385-398, 2019. PMCID6692293

397.

2019

H. Wu, D.J. Saltzberg, H.T. Kratochvil, H. Jo, A. Sali, W.F. DeGrado. Glutamine Side Chain 13C═18O as a Nonperturbative IR Probe of Amyloid Fibril Hydration and Assembly. J Am Chem Soc 141, 7320-7326, 2019. PMCID6800148

398.

2019

H.M. Berman, P.D. Adams, A.A. Bonvin, S.K. Burley, B. Carragher, W. Wah Chiu, F. DiMaio, T.E. Ferrin, M.J. Gabanyi, T.D. Goddard, P.R. Griffin, J. Haas, C.A. Hanke, J.C. Hoch, G. Hummer, G. Kurisu, C.L. Lawson, A. Leitner, J.L. Markley, J. Meiler, G.T. Montelione, Jr. Phillips GN, T. Prisner, J. Rappsilber, D.C. Schriemer, T. Schwede, C.A.M. Seidel, T.S. Strutzenberg, D.I. Svergun, E. Tajkhorshid, J. Trewhella, B. Vallat, S. Velankar, G.W. Vuister, B. Webb, J.D. Westbrook, K.L. White, A. Sali. Federating Structural Models And Data: Outcomes From A Workshop On Archiving Integrative Structures. Structure 27, 1745-1759, 2019. PMCID7108332

399.

2019

D.J. Saltzberg, M. Hepburn, K.B. Pilla, D.C. Schriemer, S.P. Lees-Miller, T.L. Blundell, A. Sali. SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange. Prog Biophys Mol Biol 147, 92-102, 2019. PMCID6903780

400.

2020

C. Gutierrez, I.E. Chemmama, H. Mao, C. Yu, I. Echeverria, S.A. Block, S.D. Rychnovsky, N. Zheng, A. Sali, L. Huang. Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling. Proc Natl Acad Sci U S A 117, 4088-4098, 2020. PMCID7049115

401.

2020

S.J. Ganesan, M.J. Feyder, I.E. Chemmama, F. Fang, M.P. Rout, B.T. Chait, Y. Shi, M. Munson, A. Sali. Integrative Structure and Function of the Yeast Exocyst Complex. Protein Sci 29, 1486-1501, 2020. PMCID7255525

402.

2020

D.E. Gordon, G.M. Jang, M. Bouhaddou, J. Xu, K. Obernier, M.J. O’Meara, J.Z. Guo, D.L. Swaney, T.A. Tummino, R. Hüttenhain, R.M. Kaake, A.L. Richards, B. Tutuncuoglu, H. Foussard, J. Batra, K. Haas, M. Modak, M. Kim, P. Haas, B.J. Polacco, H. Braberg, J.M. Fabius, M. Eckhardt, M. Soucheray, M.J. Bennett, M. Cakir, M.J McGregor, Q. Li, Z.Z.C. Naing, Y. Zhou, S. Peng, I.T. Kirby, J.E. Melnyk, J.S. Chorba, K. Lou, S.A. Dai, W. Shen, Y. Shi, Z. Zhang, I. Barrio-Hernandez, D. Memon, C. Hernandez-Armenta, C.J.P. Mathy, T. Perica, K.B. Pilla, S.J. Ganesan, D.J. Saltzberg, R. Ramachandran, X. Liu, S.B. Rosenthal, L. Calviello, S. Venkataramanan, Y. Lin, S.A. Wankowicz, M. Bohn, R. Trenker, J.M. Young, D. Cavero, J. Hiatt, T. Roth, U. Rathore, A. Subramanian, J. Noack, M. Hubert, F. Roesch, T. Vallet, B. Meyer, K.M. White, L. Miorin, D. Agard, M. Emerman, D. Ruggero, A. García-Sastre, N. Jura, M. Zastrow, J. Taunton, O. Schwartz, M. Vignuzzi, C. d’Enfert, S. Mukherjee, M. Jacobson, H.S. Malik, D.G. Fujimori, T. Ideker, C.S. Craik, S. Floor, J.S. Fraser, J. Gross, A. Sali, T. Kortemme, P. Beltrao, K. Shokat, B.K. Shoichet, N.J. Krogan. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583, 459-468, 2020. PMCID7431030

403.

2020

Y. Kwon, R. Kaake, I. Echeverria, M. Suarez, M.K. Shamsabadi, C. Stoneham, P.W. Ramirez, J. Kress, R. Singh, A. Sali, N. Krogan, J. Guatelli, X. Jia. Structural Basis of CD4 Downregulation by HIV-1 Nef. Nat Struct Mol Biol, 2020. PMCID7483821

404.

2020

F.D. Mast, A.T. Navare, A.M. van der Sloot, J. Coulombe-Huntington, M.P. Rout, N.S. Baliga, A. Kaushansky, B.T. Chait, A. Aderem, C.M. Rice, A. Sali, M. Tyers, J.D. Aitchison. Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality. J Cell Biol 219, 2020. PMCID7659715

405.

2020

Y. Qiao, Z. Wang, F. Tan, J. Chen, J. Lin, J. Yang, H. Li, X. Wang, A. Sali, L. Zhang, G. Zhong. Enhancer Reprogramming within Pre-existing Topologically Associated Domains Promotes TGF-β-Induced EMT and Cancer Metastasis. Mol Ther 28, 2083-2095, 2020

406.

2020

H. Braberg, I. Echeverria, S. Bohn, P. Cimermancic, A. Shiver, R. Alexander, J. Xu, M. Shales, R. Dronamraju, S. Jiang, G. Dwivedi, D. Bogdanoff, K.K. Chaung, R. Hüttenhain, S. Wang, . Mavor, . D, R. Pellarin, D. Schneidman, J.S. Bader, J.S. Fraser, J. Morris, J.E. Haber, B.D. Strahl, C.A. Gross, J. Dai, J.D. Boeke, A. Sali, N.J. Krogan. Genetic interaction mapping informs integrative structure determination of protein complexes. Science 370, 2020.

407.

2020

A. Leitner, A.M.J.J. Bonvin, C.H. Borchers, R.J. Chalkley, J. Chamot-Rooke, C.W. Combe, J. Cox, M. Dong, L. Fischer, M. Götze, F.C. Gozzo, A.J.R. Heck, M.R. Hoopmann, L. Huang, Y. Ishihama, A.R. Jones, N. Kalisman, O. Kohlbacher, K. Mechtler, R.L. Moritz, E. Netz, P. Novak, E. Petrotchenko, A. Sali, R.A. Scheltema, C. Schmidt, D. Schriemer, A. Sinz, F. Sobott, F. Stengel, K. Thalassinos, H. Urlaub, R. Viner, J.A. Vizcaíno, M.R. Wilkins, J. Rappsilber. Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry. Structure 28, 1259-1268, 2020.

408.

2020

K.L. White, J. Singla, V. Loconte, J.H. Chen, A. Ekman, L. Sun, X. Zhang, J.P. Francis, A. Li, W. Lin, K. Tseng, G. McDermott, F. Alber, A. Sali, C. Larabell, R.C. Stevens. Visualizing subcellular rearrangements in intact β cells using soft x-ray tomography. Sci Adv 6, 2020. PMCID7725475

409.

2020

M. Hepburn, D.J. Saltzberg, L. Lee, S. Fang, C. Atkinson, N.C.J. Strynadka, A. Sali, S.P. Lees-Miller, D.C. Schriemer. The active DNA-PK holoenzyme occupies a tensed state in a staggered synaptic complex. Structure, 2020.

410.

2021

T.H. Tran, J.V. Nguyen, A. Stecula, J. Akutagawa, A.V. Moorman, B.S. Braun, A. Sali, C.G. Mullighan, N.P. Shah, Y. Dai, M. Devidas, K.G. Roberts, C.C. Smith, M.L. Loh. The EBF1-PDGFRB T681I mutation is highly resistant to imatinib and dasatinib in vitro and detectable in clinical samples prior to treatment. Haematologica, in press, 2021.

411.

2021

S.K. Burley, C. Bhikadiya, C. Bi, S. Bittrich, L. Chen, G. Crichlow, C.H. Christie, K. Dalenberg, L. Di Costanzo, J.M. Duarte, S. Dutta, Z. Feng, S. Ganesan, D.S. Goodsell, S. Ghosh, R.K. Green, V. Guranović, D. Guzenko, B.P. Hudson, C.L. Lawson, Y. Liang, R. Lowe, H. Namkoong, E. Peisach, I. Persikova, C. Randle, A. Rose, Y. Rose, A. Sali, J. Segura, M. Sekharan, C. Shao, Y. Tao, M. Voigt, J.D. Westbrook, J.Y. Young, C. Zardecki, M. Zhuravleva. RCSB Protein Data Bank: Powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering, and energy sciences. Nucleic Acids Res 49, D437-D451, 2021. PMCID7779003

412.

2021

D.J. Saltzberg, S. Viswanath, I. Echeverria, I.E. Chemmama, B. Webb, A. Sali. Using Integrative Modeling Platform to Compute, Validate, and Archive a Model of a Protein Complex Structure. Prot Sci 30, 250-261, 2021. PMCID7737781

413.

2021

Salcedo EC, Winter MB, Khuri N, Knudsen GM, Sali A, Craik CS. Global Protease Activity Profiling Identifies HER2-Driven Proteolysis in Breast Cancer. ACS Chem Biol. 2021 Apr 16;16(4):712-723. doi: 10.1021/acschembio.0c01000. Epub 2021 Mar 25. PMID: 33765766.

414.

2021

Yu Y, Li S, Ser Z, Sanyal T, Choi K, Wan B, Kuang H, Sali A, Kentsis A, Patel DJ, Zhao X. Integrative analysis reveals unique structural and functional features of the Smc5/6 complex. Proc Natl Acad Sci U S A. 2021 May 11;118(19):e2026844118. doi: 10.1073/pnas.2026844118. PMID: 33941673; PMCID: PMC8126833.

415.

2021

Raveh B, Sun L, White KL, Sanyal T, Tempkin J, Zheng D, Bharath K, Singla J, Wang C, Zhao J, Li A, Graham NA, Kesselman C, Stevens RC, Sali A. Bayesian metamodeling of complex biological systems across varying representations. Proc Natl Acad Sci U S A. 2021 Aug 31;118(35):e2104559118. doi: 10.1073/pnas.2104559118. PMID: 34453000; PMCID: PMC8536362.

416.

2021

Brilot AF, Lyon AS, Zelter A, Viswanath S, Maxwell A, MacCoss MJ, Muller EG, Sali A, Davis TN, Agard DA. CM1-driven assembly and activation of yeast γ-tubulin small complex underlies microtubule nucleation. Elife. 2021 May 5;10:e65168. doi: 10.7554/eLife.65168. PMID: 33949948; PMCID: PMC8099430.

417.

2021

Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, Keegan S, Jiler JB, Stein ME, Olinares PDB, Hatziioannou T, Sather DN, Debley JS, Fenyö D, Sali A, Bieniasz PD, Aitchison JD, Chait BT, Rout MP. Nanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2. bioRxiv [Preprint]. 2021 Apr 10:2021.04.08.438911. doi: 10.1101/2021.04.08.438911. PMID: 33851164; PMCID: PMC8043454.

418.

2021

Hepburn M, Saltzberg DJ, Lee L, Fang S, Atkinson C, Strynadka NCJ, Sali A, Lees-Miller SP, Schriemer DC. The active DNA-PK holoenzyme occupies a tensed state in a staggered synaptic complex. Structure. 2021 May 6;29(5):467-478.e6. doi: 10.1016/j.str.2020.12.006. Epub 2021 Jan 6. PMID: 33412091; PMCID: PMC8675206.

419.

2021

Otsuka S, Tempkin JOB, Politi A, Rybina A, Hossain MJ, Kueblbeck M, Callegari A, Koch B, Sali A, Ellenberg A. A quantitative map of nuclear pore assembly reveals two distinct mechanisms. bioRxiv, 2021.05.17.444137, 2021

420.

2021

Opoku-Nsiah KA, de la Pena AH, Williams SK, Chopra N, Sali A, Lander GC, Gestwicki JE. The YΦ motif defines the structure-activity relationships of human 20S proteasome activators. Nat Commun. 2022 Mar 9;13(1):1226. doi: 10.1038/s41467-022-28864-x. PMID: 35264557; PMCID: PMC8907193.

421.

2021

Sali A. From integrative structural biology to cell biology. J Biol Chem. 2021 Jan-Jun;296:100743. doi: 10.1016/j.jbc.2021.100743. Epub 2021 May 4. PMID: 33957123; PMCID: PMC8203844.

422.

2021

Kaake RM, Echeverria I, Kim SJ, Von Dollen J, Chesarino NM, Feng Y, Yu C, Ta H, Chelico L, Huang L, Gross J, Sali A, Krogan NJ. Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host-Pathogen Complexes. Mol Cell Proteomics. 2021;20:100132. doi: 10.1016/j.mcpro.2021.100132. Epub 2021 Aug 11. PMID: 34389466; PMCID: PMC8459920.

423.

2021

Ziemianowicz DS, Saltzberg D, Pells T, Crowder DA, Schräder C, Hepburn M, Sali A, Schriemer DC. IMProv: A Resource for Cross-link-Driven Structure Modeling that Accommodates Protein Dynamics. Mol Cell Proteomics. 2021;20:100139. doi: 10.1016/j.mcpro.2021.100139. Epub 2021 Aug 19. PMID: 34418567; PMCID: PMC8452774.

424.

2021

Burley SK, Bhikadiya C, Bi C, Bittrich S, Chen L, Crichlow GV, Duarte JM, Dutta S, Fayazi M, Feng Z, Flatt JW, Ganesan SJ, Goodsell DS, Ghosh S, Kramer Green R, Guranovic V, Henry J, Hudson BP, Lawson CL, Liang Y, Lowe R, Peisach E, Persikova I, Piehl DW, Rose Y, Sali A, Segura J, Sekharan M, Shao C, Vallat B, Voigt M, Westbrook JD, Whetstone S, Young JY, Zardecki C. RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. Protein Sci. 2022 Jan;31(1):187-208. doi: 10.1002/pro.4213. Epub 2021 Nov 6. PMID: 34676613; PMCID: PMC8740825.

425.

2021

Vallat B, Webb B, Fayazi M, Voinea S, Tangmunarunkit H, Ganesan SJ, Lawson CL, Westbrook JD, Kesselman C, Sali A, Berman HM. New system for archiving integrative structures. Acta Crystallogr D Struct Biol. 2021 Dec 1;77(Pt 12):1486-1496. doi: 10.1107/S2059798321010871. Epub 2021 Nov 29. PMID: 34866606; PMCID: PMC8647179.

426.

2021

Huang F, Nguyen TT, Echeverria I, Rakesh R, Cary DC, Paculova H, Sali A, Weiss A, Peterlin BM, Fujinaga K. Reversible phosphorylation of cyclin T1 promotes assembly and stability of P-TEFb. Elife. 2021 Nov 25;10:e68473. doi: 10.7554/eLife.68473. PMID: 34821217; PMCID: PMC8648303.

427.

2022

Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, Unruh J, Jaspersen SL, Chait BT, Sali A, Fernandez-Martinez J, Ludtke SJ, Villa E, Rout MP. Comprehensive structure and functional adaptations of the yeast nuclear pore complex. Cell. 2022 Jan 20;185(2):361-378.e25. doi: 10.1016/j.cell.2021.12.015. Epub 2022 Jan 3. PMID: 34982960; PMCID: PMC8928745.

428.

2022

Braberg H, Echeverria I, Kaake RM, Sali A, Krogan NJ. From systems to structure - using genetic data to model protein structures. Nat Rev Genet. 2022 Jan 10:1–13. doi: 10.1038/s41576-021-00441-w. Epub ahead of print. PMID: 35013567; PMCID: PMC8744059.

429.

2022

Belsare KD, Wu H, Mondal D, Bond A, Castillo E, Jin J, Jo H, Roush AE, Pilla KB, Sali A, Condello C, DeGrado WF. Soluble TREM2 inhibits secondary nucleation of Aβ fibrillization and enhances cellular uptake of fibrillar Aβ. Proc Natl Acad Sci U S A. 2022 Feb 1;119(5):e2114486119. doi: 10.1073/pnas.2114486119. PMID: 35082148; PMCID: PMC8812518.

430.

2022

V. Loconte, J. Singla, A. Li, J.H. Chen, A. Ekman, G. McDermott, A. Sali, M. Le Gros, K.L. White, C.A. Larabell. Soft X-ray tomography to map and quantify organelle interactions at the mesoscale. Structure 30, 510-521, 2022. PMCID9013509

431.

2022

M. Hancock, T.O. Peulen, B. Webb, B. Poon, J.S. Fraser, P. Adams, A. Sali. Integration of software tools for integrative modeling of biomolecular systems. J Struct Biol 214, 107841, 2022. PMCID9278553

432.

2022

I. Echeverria, H. Braberg, N.J. Krogan, A. Sali. Integrative structure determination of histones H3 and H4 using genetic interactions. FEBS J, 2022. PMCID9481981

433.

2022

A. Rafiei, L. Lee, D.A. Crowder, D.J. Saltzberg, A. Sali, G.J. Brouhard, D.C. Schriemer. Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C-terminal domain. eLife 11, e66975, 2022. PMCID9122500

434.

2022

A. Li, X. Zhang, J. Singla, K. White, V. Loconte, C. Hu, C. Zhang, S. Li, W. Li, J.P. Francis, C. Wang, A. Sali, L. Sun, X. He, R.C. Stevens. Auto-segmentation and time-dependent systematic analysis of mesoscale cellular structure in β-cells during insulin secretion. PLoS One 17, e0265567, 2022. PMCID8947144

435.

2022

S. Burley, C. Bhikadiya, C. Bi, S. Bittrich, H. Chao, L. Chen, P. Craig, G. Crichlow, K. Dalenberg, J.M. Duarte, S. Dutta, M. Fayazi, Z. Feng, J. Flatt, S. Ganesan, S. Ghosh, D. Goodsell, R.K. Green, V. Guranovic, J. Henry, B. Hudson, C. Lawson, Y. Liang, R. Lowe, E. Peisach, I. Persikova, D. Piehl, Y. Rose, A. Sali, J. Segura, M. Sekharan, C. Shao, B. Vallat, M. Voigt, B. Webb, J. Westbrook, S. Whetstone, J. Young, A. Zalevsky, C. Zardecki. RCSB Protein Data Bank: Tools for visualizing and understanding biological macromolecules in 3D. Prot Sci 31, e4482, 2022. PMCID9667899

436.

2022

K.A. Opoku-Nsiah, A.H. de la Pena, S.K. Williams, N. Chopra, A. Sali, G.C. Lander, J.E. Gestwicki. The YΦ Motif Defines the Structure-Activity Relationships of Human 20S Proteasome Activators. Nat Commun 13, 1226, 2022. PMCID8907193

437.

2022

S.K. Burley, H.M. Berman, J.M. Duarte, Z. Feng, J.W. Flatt, B.P. Hudson, R. Lowe, E. Peisach, D.W. Piehl, Y. Rose, A. Sali, M. Sekharan, C. Shao, B. Vallat, M. Voigt, J.D. Westbrook, J. Young, C. Zardecki. Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students. Biomolecules 12, 1425, 2022. PMCID9599165

438.

2022

S.K. Burley, H.M. Berman, W. Chiu, W. Dai, J.W. Flatt, B.P. Hudson, J.T. Kaelber, S.D. Khare, A.W. Kulczyk, C.L. Lawson, G.D. Pintilie, A. Sali, B. Vallat, J.D. Westbrook, J.Y. Young, C. Zardecki. Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future. Biophys Rev 14, 1281-1301, 2022. PMCID9715422

439.

2022

A. Guo, J. Zhang, B. He, A. Li, T. Sun, C. Li, J. Wang, R. Tai, J. Fan, A. Sali, R.C. Stevens, H. Jiang. Quantitative, in situ visualization of intracellular insulin vesicles in pancreatic β cells. Proc Natl Acad Sci USA 119, e2202695119, 2022. PMCID9371705

440.

2023

S. Otsuka, J.O.B. Tempkin, W. Zhang, A.Z. Politi, A. Rybina, M.J. Hossain, M. Kueblbeck, A. Callegari, B. Koch, N.R. Morero, A. Sali, J. Ellenberg. A quantitative map of nuclear pore assembly reveals two distinct mechanisms. Nature 613, 575-581, 2023. PMCID9849139

441.

2023

B. Vallat, G. Tauriello, S. Bienert, J. Haas, B.M. Webb, A. Žídek, W. Zheng, E. Peisach, D.W. Piehl, I. Anischanka, I. Sillitoe, J. Tolchard, M. Varadi, D. Baker, C. Orengo, Y. Zhang, J.C. Hoch, G. Kurisu, A. Patwardhan, S. Velankar, S.K. Burley, A. Sali, T. Schwede, H.M. Berman, J.D. Westbrook. ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models. J Mol Biol 435, 168021, 2023. PMCID10293049

442.

2023

T. Kozai, J. Fernandez-Martinez, T. van Eeuwen, P. Gallardo, L.E. Kapinos, A. Mazur, W. Zhang, J. Tempkin, M. Delgado-Izquierdo, B. Raveh, A. Sali, B.T. Chait, L.M. Veenhoff, M.P. Rout, R.Y.H. Lim. Dynamic molecular mechanism of the nuclear pore complex permeability barrier.bioRxiv [Preprint]. 2023 Apr 14:2023.03.31.535055 PMCID10103940

443.

2023

K.H. Burns, B. Smail, H. Jiang, A. Zalevsky, N. Dai, R.J. Trachman, S. Guan, A. Sali, M.S. Taylor, J. LaCava. Robust cleavage of mismatched DNA by the LINE-1 endonuclease. J Biol Chem, in press, 2023.

444.

2023

S.K. Kim, M.S. Dickinson, J. Finer-Moore, Z. Guan, R.M. Kaake, I. Echeverria, J. Chen, E.H. Pulido, A. Sali, N.J. Krogan, O.S. Rosenberg, R.M. Stroud. Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13. Nat Struct Mol Biol 30, 296-308, 2023. PMCID10312659

445.

2023

C.W. Akey, I. Echeverria, C. Ouch, I. Nudelman, Y. Shi, J. Wang, B.T. Chait, A. Sali, J. Fernandez-Martinez, M.P. Rout. Implications of a multiscale structure of the yeast nuclear pore complex. Mol Cell 83, 3283-3302.e5, 2023. PMCID10630966

446.

2023

T.O. Peulen, A. Sali. Bayesian Fluorescence Framework for integrative modeling of biomolecules. in press, 2023.

447.

2023

Z. Lin, K. Schaefer, I. Lui, Z. Yao, A.A. Fossati, D.L. Swaney, A. Palar, A. Sali, J.A. Wells. Multi-scale photocatalytic proximity labeling reveals cell surface neighbors on and between cells. in press, 2023

448.

2023

E.T. Baldwin, T. van Eeuwen, D. Hoyos, A. Zalevsky, E.P. Tchesnokov, R. Sánchez, B.D. Miller, L.H. Di Stefano, F.X. Ruiz, M. Hancock, E. Işik, C. Mendez-Dorantes, T. Walpole, C. Nichols, P. Wan, K. Riento, R. Halls-Kass, M. Augustin, A. Lammens, A. Jestel, P. Upla, K. Xibinaku, S. Congreve, M. Hennink, K.B. Rogala, A.M. Schneider, J.E. Fairman, S.M. Christensen, B. Desrosiers, G.S. Bisacchi, O.L. Saunders, N. Hafeez, W. Miao, R. Kapeller, D.M. Zaller, A. Sali, O. Weichenrieder, K.H. Burns, M. Götte, M.P. Rout, E. Arnold, B.D. Greenbaum, D.L. Romero, J. LaCava, M.S. Taylor. Structures, functions, and adaptations of the human LINE-1 ORF2 protein. Nature 626, 194-206, 2023. PMCID10830420

449.

2024

N.E. Ketaren, F.D. Mast, P.C. Fridy, J.P. Olivier, T. Sanyal, A. Sali, B.T. Chait, M.P. Rout, J.D. Aitchison. Nanobody repertoire generated against the spike protein of ancestral SARS-CoV-2 remains efficacious against the rapidly evolving virus. eLife 12, RP89423, 2024. PMCID1107604

450.

2024

S. Pourmal, E. Green, R. Bajaj, I. Chemmama, G.M. Knudsen, M. Gupta, A. Sali, Y. Cheng, C.S. Craik, R.M. Stroud, D.L. Kroetz. Structural Basis of Prostaglandin Efflux by MRP4. Nat Struct Mol Biol 31, 621-632, 2024.

451.

2024

W. Li, A. Li, B. Yu, X. Zhang, X. Liu, K.L. White, R.C. Stevens, W. Baumeister, A. Sali, M. Jasnin, L. Sun. In situ structure of actin remodeling during glucose-stimulated insulin secretion using cryo-electron tomography. Nat Commun 15, 1311, 2024. PMCID10861521

452.

2024

B. Raveh, R. Eliasian, S. Rashkovits, D. Russel, R. Hayama, S.E. Sparks, D. Singh, R. Lim, E. Villa, M.P. Rout, D. Cowburn, A. Sali. Integrative spatiotemporal map of nucleocytoplasmic transport. in press, 2024. PMCID10802240

453.

2024

B. Vallat, B.M. Webb, J.D. Westbrook, T.D. Goddard, C.A. Hanke, A. Graziadei, E. Peisach, A. Zalevsky, J. Sagendorf, H. Tangmunarunkit, S. Voinea, M. Sekharan, J. Yu, A.A.M.J.J. Bonvin, F. DiMaio, G. Hummer, J. Meiler, E. Tajkhorshid, T.E. Ferrin, C.L. Lawson, A. Leitner, J. Rappsilber, C.A.M. Seidel, C.M. Jeffries, S.K. Burley, J.C. Hoch, G. Kurisu, K. Morris, A. Patwardhan, S. Velankar, T. Schwede, J. Trewhella, C. Kesselman, H.M. Berman, A. Sali. IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. J Mol Biol 436, 168546, 2024

454.

2024

D. Singh, N. Soni, J. Hutchings, I. Echeverria, F. Shaikh, M. Duquette, S. Suslov, Z. Li, T. van Eeuwen, K. Molloy, Y. Shi, J. Wang, Q. Guo, B.T. Chait, J. Fernandez-Martinez, M.P. Rout, A. Sali, E. Villa. The Molecular Architecture of the Nuclear Basket. Cell 187, 5267-5281, 2024. PMCID11416316

455.

2024

K. Giacomini, S.W. Yee, L.F. Peral, P. Alentorn-Moron, C. Fontsere, M. Ceylan, M. Koleske, N. Handin, V. Artegoitia, G. Lara, H. Chien, X. Zhou, J. Dainat, A. Zalevsky, A. Sali, C. Brand, J. Capra, P. Artursson, J. Newman, T. Marques-Bonet, F. Wolfreys, J. Yang, J. Gestwicki. Illuminating the Function of the Orphan Transporter, SLC22A10, in Humans and Other Primates. Nat Comm, in press, 2024. PMCID10543398

456.

2024

T. Clark, J. Mohan, L. Schaffer, K. Obernier, S. Al Manir, C.P. Churas, A. Dailamy, Y. Doctor, A. Forget, J.N. Hansen, M. Hu, J. Lenkiewicz, M.A. Levinson, C. Marquez, S. Nourreddine, J. Niestroy, D. Pratt, G. Qian, S. Thaker, J. Bélisle-Pipon, C. Brandt, J. Chen, Y. Ding, S. Fodeh, N. Krogan, E. Lundberg, P. Mali, P. Payne-Foster, S. Ratcliffe, V. Ravitsky, A. Sali, W. Schulz, T. Ideker. Cell Maps for Artificial Intelligence: AI-Ready Maps of Human Cell Architecture from Disease-Relevant Cell Lines. in press, 2024. PMCID11142054

457.

2024

C.A. Hanke, J.D. Westbrook, B.M. Webb, T. Peulen, C.L. Lawson, A. Sali, H.M. Berman, C.A.M. Seidel, B. Vallat. Making fluorescence-based integrative structures and associated kinetic information accessible. Nat Meth, online ahead of print, 2024

458.

2024

A.P. Latham, J.O.B. Tempkin, S. Otsuka, W. Zhang, J. Ellenberg, A. Sali. Integrative spatiotemporal modeling of biomolecular processes: application to the assembly of the Nuclear Pore Complex. bioRxiv, 2024. PMCID11326192

459.

2024

T.O. Peulen, K. Hemmen, A. Greife, B.M. Webb, S. Felekyan, A. Sali, C.A.M. Seidel, H. Sanabria, K.G. Heinze. tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling. Bioinformatics, in press, 2024

SIGNIFICANT PUBLICATIONS

1.	1993	Comparative protein modelling by satisfaction of spatial restraints. A Sali, TL Blundell/> Journal of Molecular Biology 234, 779-815, 1993
2.	1994	How does a protein fold? A Sali, E. Shakhnovich, M Karplus/> Nature 369, 248-251, 1994
3.	2007	Determining the architectures of macromolecular assemblies.F Alber, S Dokudovskaya, LM Veenhoff, W Zhang, J Kipper, D Devos, .../> Nature 450 (7170), 683-694, 2007
4.	2018	Integrative Structure and Functional Anatomy of a Nuclear Pore Complex S.J. Kim, J. Fernandez-Martinez, I. Nudelman, Y. Shi, W. Zhang, B. Raveh, T. Herricks, B.D. Slaughter, J. Hogan, P. Upla, I.E. Chemmama, R. Pellarin, I. Echeverria, M. Shivaraju, A.S. Chaudhury, J. Wang, R. Williams, J.R. Unruh, C.H. Greenberg, E.Y. Jacobs, Z. Yu, M.J. de la Cruz, R. Mironska, D.L. Stokes, J.D. Aitchison, M.F. Jarrold, J.L. Gerton, S.J. Ludtke, C.W. Akey, B.T. Chait, A. Sali, M.P. Rout Nature 555, 475-482, 2018
5.	2021	B. Raveh, L. Sun, K.L. White, T. Sanyal, J. Tempkin, D. Zheng, K.B. Pilla, J. Singla, C. Wang, J. Zha, A. Li, N.A. Graham, C. Kesselman, R.C. Stevens, A. Sali. Bayesian metamodeling of complex biological systems across varying representations. Proc Natl Acad Sci USA 118, e2104559118, 2021. PMCID8536362

ACADEMIC LEADERSHIP

Dr. Sali is involved in the leadership of RCSB Protein Data Bank, the key community database in structural biology. His roles have included membership on the Scientific Advisory Board, organizing a number of PDB workshops, and contributing as well as leading the writing of White Papers that made recommendations about the organization of the PDB and validation of various types of structures deposited in the database. In particular, Dr. Sali has co-led the establishment of PDB-Dev, the nascent PDB archive for integrative structures.

Dr. Sali also plays key roles in several cell mapping efforts involving a large number of research groups, including Pancreatic Beta Cell Consortium, Cancer Cell Mapping Initiative, and Host-Pathogen Mapping Initiative.

OTHER CREATIVE ACTIVITIES

1.

OTHER MENTORING:

2004-now Coaching of iPQB student journal club presentations (approx. 3 students each year).

2006-now The Academic Advisor for approximately one third of students in BMI.

2008-now Coaching iPQB graduate students on submitting NSF research proposals.

Dates	Name	Program	Role
2004	Nima Fayazmanesh	Biophysics	Supervised Graduate Rotation
2003	Greg Friedland	Biophysics	Supervised Graduate Rotation
2005	Michael Mysinger	PSPG	Supervised Graduate Rotation
2004	Dale Webster	BMI	Supervised Graduate Rotation
2003	Alex Adai	BMI	Supervised Graduate Rotation
2003	Brian Tuch	BMI	Supervised Graduate Rotation
2006	Alan Barber	PSPG	Supervised Graduate Rotation
2008	Adam Marko	BMI	Supervised Graduate Rotation
2008	Rocco Varela	BMI	Supervised Graduate Rotation
2004	Tiba Ayunechi	BMI	Thesis Committee member
2004	Barbara Novak	BMI	Orals Committee member
2004	Alan Graves	Biophysics	Orals Committee member
2004-now	Alexandra Schnoes	BMI	Orals, thesis Committee member
2005	Ben Sellers	Biophysics	Orals Committee member
2005	Nathan Salomonis	PSPG	Orals Committee member
2005	Jerome Nilmeir	Biophysics	Orals Committee member
2005-07	Tuan Pham	BMI	Orals, Thesis Committee member
2006-07	Marco Sorani	BMI	Thesis committee member
2006-07	David Lomelin	BMI	Orals Committee member
2006-08	Ben Sellers	BMI	Thesis committee member
2006	Nima Fayazmanesh	Biophysics	Orals Committee member
2006	Arjun Narayanan	Biophysics	Orals Committee member
2006	Veena Thomas	PSPG	Orals Committee member
2006	Dale Webster	BMI	Orals Committee member
2006	Holly Atkinson	BMI	Orals Committee member
2006	Dan Mandel	BMI	Orals Committee member
2006-now	Mike Keiser	BMI	Orals, Thesis Committee Member
2007-now	Elisabeth Humphris	Biophysics	Orals, Thesis Committee member
2007-now	Colin A. Smith	BMI	Orals Committee member
2005-08	Greg Friedland	Biophysics	Orals, Thesis Committee member
2007	Rafaela Ferreira	BMI	Orals Committee member
2007	Michelle Dimon	BMI	Orals Committee member
2007	Michael Hicks	PSPG	Orals Committee member
2008	Matt Eames	Biophysics	Thesis Committee member
2008	Jason Fernandez	PSPG	Orals Committee member
2008	Leonard Apeltsin	BMI	Orals, Thesis Committee member
2009	Alan Barber	PSPG	Orals Committee member
2009	Hannes Braberg	Biophysics	Orals Committee member
2009	Noah Ollikainen	BMI	Orals, Thesis Committee member
2009	Peter Skewes-Cox	BMI	Orals Committee member
2009	Monica Tremont	Biophysics	Orals Committee member
2009	Kiyoshi Egami	Biophysics	Orals Committee member
2009	Martin Turk		Visiting Scholar
2010	Rocco Varela	BMI	Thesis Committee member
2010	Russell Spitzer	BMI	Orals Committee member
2010	Henry Lin	BMI	Orals Committee member
2010	Jeremy Phillips	BMI	Thesis Committee member
2010	Geoff Rollins	Biophysics	Orals Committee member
2010	Laurens Kraal	BMI	Orals Committee member
2010	Ethan Geier	PSPG	Orals Committee member
2010	Davide Bau		Visiting Scholar
2010	Benjamin Schwartz		Visiting Scholar
2010	Yannick Spill		Visting Scholar
2011	Brittany Fotsch	CCB	Supervised Graduate Rotation
2011	Zac Apte	Biophysics	Orals Committee member
2011	Yi Song	BMI	Supervised Graduate Rotation
2011	Argyris Politis		Visiting Scholar
2011	Amrita Choudhury		Visiting Scholar
2011	Javona White Bear	BMI	Supervised Graduate Rotation
2011	Natalia Khuri	Biophysics	Supervised Graduate Rotation
2011	Pia Unverdorben		Visiting Scholar
2011	Bart Lenselink		Visiting Scholar
2011	Yannick Spill		Visiting Scholar
2012	Sara Calhoun	Biophysics	Supervised Graduate Rotation
2012	Diego Garrido Ruiz	Biophysics	Supervised Graduate Rotation
2012	Kale Kundert	Biophysics	Supervised Graduate Rotation
2012	Adrian Stecula	PSPG	Supervised Graduate Rotation
2012	Miriam Sgobba		Visiting Scholar
2012	Jeff Yunes	Bioengineering	Orals Committee member
2012	James Webber	BMI	Orals Committee member
2013	Kyle Barlow	iPQB	Orals Committee member
2013	Joel Karpiak	CCB	Orals Committee member
2013	Rahel Woldeyes	CCB	Orals Committee member
2013	Andrew Vanbenschoten	Biophysics	Thesis Committee member
2013	Daniel Himmelstein	BMI	Orals Committee member
2014	Dorota Latek		Visiting Scholar
2014	Ilan Chemmama	Biophysics	Supervised Graduate Rotation
2014	Melissa Lemke		Visiting Scholar
2014	Reed Stein	PSPG	Supervised Summer Rotation
2014	Leo Gendelev	Biophysics	Orals Committee member
2014	Ibai Irastorza		Visiting Scholar
2015	Yiran Wu		Visiting Scholar
2015	Seth Axen	Bioinformatics	Supervised Graduate Rotation
2015	Leon Bichman		Visiting Scholar
2015	Sam Ivry	PSPG	Quals Committee Member
2015	Rebecca Davidson	BMI	Quals Committee Member
2015	Neville Bethel	Biophysics	Quals Committee Member
2015	Sara Calhoun	Biophysics	Thesis Committee Member
2015	Diego Garrido Ruiz	Biophysics	Thesis Committee Member
2015	Kale Kundert	Biophysics	Thesis Committee Member
2016	Daniel Himmelstein	Bioinformatics	Thesis Committee Member
2016	Ilan Chemmama	Biophysics	Thesis Committee Member
2016	Charles Greenberg	Biophysics	Thesis Committee Member
2016	Bruk Mensa	CCB	Quals Committee Member
2016	James Webber	BMI	Quals Committee Member
2016	Elena Caceres	BMI	Quals Committee Member
2016	Kyle Barlow	BMI	Thesis Committee Member
2017	Kale Kundert	Biophysics	Thesis Committee Member
2017	Charlotte Nelson	BMI	Thesis Committee Member
2017	Alexander Wolff	Biophysics	Thesis Committee Member
2017	Benjamin Barad	Biophysics	Thesis Committee Member
2018	James Lucas	Bioengineering	Thesis Committee Member
2018	Cole Helsell	iPQB	Academic Advisor
2018	Bryan Faust	Biophysical	Academic Advisor
2018	Laurel Estes	iPQB	Academic Advisor
2018	Wren Saylor	iPQB	Academic Advisor
2018	Stephanie Wankowicz	BMI	Academic Advisor
2018	Nick Hoppe	Biophysical	Academic Advisor
2019	Cody Krivacic	Bioengineering	Thesis Committeee Member

FORMAL COURSES ELSEWHERE:

· Instructor for a one semester graduate course “Analysis and prediction of protein structures” at The Rockefeller University, in 1998 and 2000.

· Guest lecturer at courses and workshops at Rockefeller University (1995-2018), Weill Medical College of Cornell University (1999-2002), New York University (2000-2002), Crystallography School in Erice, Italy (1999, 2008), FEBS course in Barcelona, Spain (1990), Stanford University (2002), Institute for Systems Biology (2006 and 2007), and Scripps Institute (annually since 2010)

ADDITIONAL RELEVANT INFORMATION

ORGANIZATION OF MEETINGS:

1999-2001	Program Committee, Georgia Tech Intl. Conference on Bioinformatics, Atlanta GA
2001	Program Committee, Math/Chem/Comp 2001, Dubrovnik, Croatia
2005	Program Committee, Protein Society 19th Symposium in Boston, MA
2005	Program Committee, Protein Structure Modeling Workshop, Rutgers University,NJ
2006	Program Committee, American Society for Biochemistry and Molecular Biology
2007	Program Committee, 4th Conference on Modeling of Protein Interactions (MPI)
2008	Organizer, Workshop on Applications of Protein Structure Models in Biomedical Research,
	UCSF, CA
2010	Program Committee, 3DSIG symposium at ISMB conference, Boston
2010	Co-Organizer, Keystone Symposia on Frontiers in Structural Biology
2012	Co-Organizer, Keystone Symposia on High-Throughput Structural Biology
2012	Co-Organizer, Conference on Structural Analysis of Supramolecular Assemblies by Hybrid Methods, Lake Tahoe
2013	Organizer, Keystone Symposia on Structural Analysis of Supramolecular Assemblies by Hybrid Methods, Lake Tahoe
2014	Organizer, Martin Karplus Celebration Symposium
2006-now 2019	Organizer, World Molecular Engineering Network, annual TSRI & UCSF meeting in San Jose del Cabo, Mexico Organizer, 63rd Annual Meeting of the Biophysical Society, Baltimore, MD, Mar 2-6, 2019.

FELLOWSHIPS TO LAB MEMBERS:

Howard Hughes Predoctoral Fellowship (R. Sanchez)

Howard Hughes Predoctoral Fellowship (F. Davis)

Burroughs Wellcome Fund Predoctoral Fellowship (R. Chiang)

Alfred P. Sloan Postdoctoral Fellowship (A. Stuart)

Burroughs Wellcome Fund Postdoctoral Fellowship (A. Fiser, M.A. Marti-Renom)

Rockefeller University Presidential Fellowship (M.A. Marti-Renom)

Charles Revson Foundation Postdoctoral Fellowship (A. Fiser, M.S. Madhusudhan)

NIH Postdoctoral Fellowship (R. Karchin)

Burroughs Wellcome Predoctoral Fellowship (M. Kim, R. Chiang)

DOE Predoctoral Fellowship (M. Peterson)

Genentech Award (M. Peterson)

Human Frontier Sciences Program Postdoctoral Fellowship (F. Foerster)

Spanish Minister of Education Postdoctoral Fellowship (J. Velazquez)

Clore Foundation Predoctoral Fellowship (K. Lasker)

Weizmann Institute Advancing Women in Science Postdoctoral Fellowship (D. Schneidman)

UC Cancer Research Coordinating Committee Fellowship (D. Barkan)

NIH NRSA Postdoctoral Fellowship (A. Schlessinger)

Chancellor’s Graduate Research Fellowship (P. Cimermancic)

Swiss National Science Foundation Perspective Researcher Fellowship (R. Pellarin)

NSC Taiwan Postdoctoral Fellowship (B. Chen)

NSF Graduate Research Fellowship (C. Greenberg)

Howard Hughes Medical Institutes Predoctoral Fellowship (P. Cimermancic)

Frank M. Goyan Award for Excellence in Physical Chemistry (J. Phillips)

2012 School of Pharmacy Research Award (P. Cimermancic)

QB3 Rogers Award (P. Cimermancic)

NIH Fellowship (K. Stafford)

PhRMA Fellowship in Pharmacology/Toxicology (A. Stecula)

Mel Jones Excellence in Graduate Student Research Award (C. Greenberg)

PhRMA Fellowship in Pharmacology/Toxicology (A. Stecula)

AFPE Pre-Doctoral Award in Pharmaceutical Science (A. Stecula)

NSF Fellowship (Ilan Chemmama)

NSF Fellowship (Seth Axen)

EMBL postdoctoral fellowship (Jeremy Tempkin)

SOFTWARE:

1993 MODELLER, a program for comparative protein structure modeling by satisfaction of spatial restraints; licensed to Accelrys Inc. since 1994.

2000 MODPIPE, a program for large-scale comparative protein structure modeling; licensed to Accelrys Inc. and Structural Genomix Pharmaceuticals Inc. (2000-2004).

2000 MODBASE, a comprehensive database of comparative protein structure models; licensed to Structural Genomix Pharmaceuticals Inc. (2000-2004).

2010 IMP, a program for integrative structure determination of macromolecular assemblies, open source.

Companies Founded

Prospect Genomix, 1999

Global Blood Therapeutics, 2012
Quanta Therapeutics, 2018