Sali Lab logo Laboratory of Andrej Sali QB3

Integrative Structural Biology

We aim to develop and apply computational methods for integrative determination of the structures and dynamics of macromolecular assemblies, in turn informing the function and evolution of these systems as well as how to modulate them. The broad goal is to contribute to a predictive spatiotemporal model of the cell. This goal is being achieved by a formal integration of experiment, physics, and statistical inference, spanning all relevant size and time scales. Our computational methods are implemented in the open source Integrative Modeling Platform package (IMP) and the resulting models are deposited in the PDB-Dev database. This research enhances the discovery of general principles that underlie all cellular processes, which in turn also facilitates drug discovery.


Postdoctoral positions at the Quantitative Biology Institute available:
The Quantitative Biology Institute (QBI) at the University of California, San Francisco, is recruiting six postdoctoral fellows in the area of computational structural biology. See the description of these positions for more information.

PDB creates an archive for integrative structures:
wwPDB has created a new archive, PDB-Dev, for storing structural models obtained through use of integrative methods. It contains a rapidly-growing number of such models, produced with software including our own IMP package.

Congratulations to Daniel:
Daniel Saltzberg has received the Lilly Research Award!

Congratulations to SJ:
The paper "Integrative Structure and Functional Anatomy of a Nuclear Pore Complex" has been published in Nature!

Congratulations to Sara:
The paper "Prediction of enzymatic pathways by integrative pathway mapping" has been published in eLife!

Congratulations to Sara:
Sara Calhoun received the Mel Jones Excellence in Graduate Student Research Award !

Congratulations to Adrian:
Adrian Stecula is a recipient of an AFPE Pre-Doctoral Award in Pharmaceutical Science!

Congratulations to Ilan:
Ilan Chemmama has received a 3 year NSF fellowship !

Congratulations to Kate:
Kate Stafford has received a 3 year NRSA fellowship !

Congratulations to Adrian:
Adrian is a recipient of the PhRMA fellowship in Pharmacology/Toxicology !

Congratulations to Jeremy Horst: His recent publication was highlighted by the Structural Biology Knowledgebase.

Workshop on Theoretical Model Archiving, Validation and PDBx/mmCIF Data Exchange Format.
October 21 & 22, 2013
Rutgers University, NJ.

Congratulations to Natalia:
Natalia is a recipient of a 2013-2014 Merit Fellowship Award - an Achievement Rewards for College Scientists (ARCS) Scholarship !

Congratulations to SJ:
The paper "Structure, Dynamics, Evolution, and Function of a Major Scaffold Component in the Nuclear Pore Complex", P. Sampathkumar, et al, has been published in Structure! We also congratulate Graham Johnson of UCSF for the great cover image!

Congratulations to Javi:
We wish him the best in his position as Bioinformatics Analyst at Cypher Genomics!

Congratulations to Avner:
We wish him the best in his new position as Assistant Professor at Mount Sinai Hospital !

Congratulations to Jeremy and Peter:
Jeremy won the Frank M. Goyan Award for Excellence in Physical Chemistry and Peter has received the 2012 School of Pharmacy Research Award !

Congratulations to Keren:
The paper "Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach", K. Lasker, et al, has been accepted for publication in PNAS !

Congratulations to Riccardo on the news of his Swiss National Science Foundation fellowship!!

Congratulations to Avner:
The paper "Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET", A. Schlessinger, E. Geier, H. Fan, J. Irwin, B. Shoichet, K. Giacomini, A. Sali, has been accepted for publication in PNAS !

Congratulations to Peter on being awarded the Howard Hughes Medical Institutes Predoctoral Fellowship!!

Congratulations Charles on being awarded the NSF Graduate Research Fellowship!!

Selected Publications

  • 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. PubMed PDF
  • 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. PubMed PDF
  • 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. PubMed ...
  • A. Sali. "From integrative structural biology to cell biology" J Biol Chem 100743, 2021. PubMed PDF


Transport through the NPC Ribosome Cell modeling Example protein structure Protein-ligand docking Docking of comparative models Localization density map of the NPC, side view Localization density map of the NPC, top view Deterining the structures of proteins and macromolecular assemblies Flagellar motor Goal of modeling Mindset of modeling Using all spatial information Structure determination of macromolecular assemblies Characterizing structures by satisfaction of spatial restraints IMP building blocks Compariatve protein structure modeling Principles of protein structure Model accuracy determines utility Modeller flowchart Molecular motor model Errors in comparative models vs. resolution Protein structure modeling in an EM map S. cerevisiae ribosome What is known about the NPC structure? Protein localization probability and volume Configuration of 456 proteins in the Nuclear Pore Complex Configuration of proteins in NPC? Use all information Assembling the NPC structure Side view of transport through the NPC Protein structure fitted into an EM map Module architecture of the NPC Point model of the NPC Localization of all NPC proteins Architecture of the NPC Assembly of subunits by combining restraints with optimization Membrane protein Assembly of the NPC
Andrej Sali, PhD, Professor, Department of Bioengineering and Therapeutic Sciences; Department of Pharmaceutical Chemistry; School of Pharmacy, University of California at San Francisco, UCSF MC 2552, Mission Bay, Byers Hall, 1700 4th Street, Suite 503B, San Francisco, CA 94143, Tel +1 (415) 514-4227, Fax +1 (415) 514-4231, 4234, , Web

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