Andrej Sali Lab

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234.	T. Lezon, A. Sali, I. Bahar. Global motions of the nuclear pore complex:Insights from Elastic Network Models. PLoS Computational Biology, in press.
233.	D. Barkan, D. Hostetter, S. Mahrus, U. Pieper, J. Wells, C. Craik, A. Sali. Prediction of Protease Substrates using Sequence and Structural Features. submitted.
232.	D.J. Taylor, B. Devkota, A.D. Huang, M. Topf, N. Eswar, A. Sali, S.C. Harvey, J. Frank. Comprehensive Atomic Model of the Eukaryotic Ribosome. submitted.
231.	F.P. Davis, A. Sali. The overlap of small molecule and protein binding sites within families of protein structures. submitted.
230.	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. Molecular Architecture of the 26S Proteasome. Proceedings of the National Academy of Sciences USA, in press.
229.	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. PMC2687990
228.	H. Fan, N. Eswar, J.J. Irwin, A. Sali, B. Shoichet. Virtual Ligand Screening Using Comparative Models of Proteins. submitted.
227.	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. Nature Biotechnology 27, 320-321, 2009.
226.	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. Journal of Structural and Functional Genomics 10, 193-208, 2009.
225.	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. PMC2682653
224.	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 Neglected Tropical Diseases 3, e418, 2009. PMC2667270
223.	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. PMCID TBD by Journal.
222.	D. Russel, K. Lasker, J. Phillips, D. Schneidman-Duhovny, J.A. Velazquez-Muriel, A. Sali. The structural dynamics of macromolecular processes. Current Opinion in Cell Biology 21, 97-108, 2009. PMCID TBD by Journal.
221.	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 Science 18, 1306-1315, 2009. PMCID TBD by Journal.
220.	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. Journal of Molecular Biology 385, 820-830, 2009. PMC2659619
219.	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. Journal of Structural and Functional Genomics 10, 9-16, 2009.
218.	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. Molecular and Cellular Proteomics, in press, 2009.
217.	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 Research 37, D347-354, 2009. PMC2686492
216.	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. Journal of Structural and Functional Genomics 10, 107-125, 2009. PMC2693957
215.	K. Lasker, M. Topf, A. Sali, H.J. Wolfson. Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly. Journal of Molecular Biology 388, 180-194, 2009. PMC2680734
214.	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. Proceedings of the National Academy of Sciences USA 105, 9610-9615, 2008. PMC2474495
213.	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. PMC2566540
212.	R.A. Chiang, A. Sali, P.C. Babbitt. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Computational Biology 4, e1000142, 2008. PMC2453236
211.	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.
210.	M.F. Kim, A. Sali, V. Dotsch, M.L. Reese. Efficient computational identification and docking of macromolecular interfaces using ambiguous NMR constraints. submitted.
209.	M.S. Madhusudhan, M.A. Marti-Renom, N. Eswar, A. Sali. Alignment of multiple protein structures based on sequence and structure features. Protein Engineering, Design, and Selection, in press.
208.	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 and Development 22, 854-859, 2008. PMC2279195
207.	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. Journal of Molecular Biology 382, 1089-1106, 2008. PMCID TBD by Journal.
206.	L. Kelly, U. Pieper, F.A. Hays, N. Eswar, D. Kroetz, K.M. Giacomini, R.M. Stroud, A. Sali. A taxonomic profile of the membrane protein universe. Journal of Structural and Functional Genomics, in press.
205.	D. Eramian, N. Eswar, M.Y. Shen, A. Sali. How well can the accuracy of comparative protein structure models be predicted? Protein Science 17, 1881-1893, 2008. PMC2578807
204.	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. PMC2600884
203.	R. Karchin, M. Agarwal, A. Sali, F. Couch, M.S. Beattie. Classifying Variants of Undetermined Significance in BRCA2 with Protein Likelihood Ratios. Cancer Informatics 6, 203-216, 2008. PMC2587343
202.	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. Nature Reviews Drug Discovery 7, 900-907, 2008. PMCID TBD by Journal.
201.	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. PMC2430716
200.	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. PMC2409374
199.	F. Alber, F. Forster, D. Korkin, M. Topf, A. Sali. Integrating diverse data for structure determination of macromolecular assemblies. Annual Review of Biochemistry 77, 443-477, 2008.
198.	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.
197.	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.
196.	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.
195.	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. Nature Structural and Molecular Biology 15, 746-753, 2008. PMC2546500
194.	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. Journal of Molecular Biology 375, 331-336, 2008. PMC2680129
193.	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.
192.	N. Eswar, D. Eramian, B. Webb, M.Y. Shen, A. Sali. Protein structure modeling with MODELLER. Methods in Molecular Biology 426, 145-159, 2008.
191.	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.
190.	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.
189.	C.V. Robinson, A. Sali, W. Baumeister. The molecular sociology of the cell. Nature 450, 973-982, 2007.
188.	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 Protein Science Chapter 2, Unit 2 9, 2007.
187.	A. Sali, C.D. Lima, M. Kostic. Structural genomics. Structure 15, 1341, 2007.
186.	F. Melo, A. Sali. Fold assessment for comparative protein structure modeling. Protein Science 16, 2412-2426, 2007.
185.	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. Journal of Structural and Functional Genomics 8, 121-140, 2007.
184.	F.P. Davis, D.T. Barkan, N. Eswar, J.H. McKerrow, A. Sali. Host pathogen protein interactions predicted by comparative modeling. Protein Science 16, 2585-2596, 2007.
183.	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 Research 35, W393-397, 2007.
182.	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.
181.	R. Aragues, A. Sali, J. Bonet, M.A. Marti-Renom, B. Oliva. Characterization of protein hubs by inferring interacting motifs from protein interactions. PLoS Computational Biology 3, 1761-1771, 2007.
180.	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 Computational Biology 3, e241, 2007.
179.	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.
178.	E. Feyfant, A. Sali, A. Fiser. Modeling mutations in protein structures. Protein Science 16, 2030-2041, 2007.
177.	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.
176.	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 Research 67, 1494-1501, 2007.
175.	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.
174.	L. Kelly, R. Karchin, A. Sali. Protein interactions and disease phenotypes in the ABC transporter superfamily. Pacific Symposium on Biocomputing, 51-63, 2007.
173.	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.
172.	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.
171.	M.Y. Shen, A. Sali. Statistical potential for assessment and prediction of protein structures. Protein Science 15, 2507-2524, 2006.
170.	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. Journal of Molecular Biology 363, 835-857, 2006.
169.	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.
168.	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. Pharmacological Reviews 58, 1-2, 2006.
167.	F.P. Davis, H. Braberg, M.Y. Shen, U. Pieper, A. Sali, M.S. Madhusudhan. Protein complex compositions predicted by structural similarity. Nucleic Acids Research 34, 2943-2952, 2006.
166.	A. Rossi, M.A. Marti-Renom, A. Sali. Localization of binding sites in protein structures by optimization of a composite scoring function. Protein Science 15, 2366-2380, 2006.
165.	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.
164.	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.
163.	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 Science 15, 1653-1666, 2006.
162.	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.
161.	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. Journal of Molecular Biology 357, 1655-1668, 2006.
160.	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 Research 34, D291-295, 2006.
159.	C. Lima, J. Puglisi, A. Sali, L. Szewczak. Editorial. Structure 14, 801, 2006.
158.	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.
157.	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. Proceedings of the National Academy of Sciences U S A 103, 2172-2177, 2006.
156.	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.
155.	M. Topf, A. Sali. Combining electron microscopy and comparative protein structure modeling. Current Opinion in Structural Biology 15, 578-585, 2005.
154.	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. Journal of Structural and Functional Genomics 6, 225-232, 2005.
153.	M.Y. Shen, F.P. Davis, A. Sali. The optimal size of a globular protein domain: A simple sphere-packing model. Chemical Physics Letters 405, 224-228, 2005.
152.	D. Korkin, F.P. Davis, A. Sali. Localization of protein-binding sites within families of proteins. Protein Science 14, 2350-2360, 2005.
151.	A. Sali, W. Chiu. Macromolecular assemblies highlighted. Structure 13, 339-341, 2005.
150.	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.
149.	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.
148.	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.
147.	F.P. Davis, A. Sali. PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics 21, 1901-1907, 2005.
146.	F. Alber, M.F. Kim, A. Sali. Structural characterization of assemblies from overall shape and subcomplex compositions. Structure 13, 435-445, 2005.
145.	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.
144.	R. Karchin, L. Kelly, A. Sali. Improving functional annotation of non-synonomous SNPs with information theory. Pacific Symposium on Biocomputing, 397-408, 2005.
143.	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. Journal of Structural Biology 149, 191-203, 2005.
142.	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. Proceedings of the National Academy of Sciences U S A 102, 7151-7156, 2005.
141.	S.M. Maurer, A. Rai, A. Sali. Finding Cures for Tropical Diseases: Is Open Source an Answer? PLoS Medicine 1, e56, 2004.
140.	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.
139.	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. Current Opinion in Structural Biology 14, 313-324, 2004.
138.	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.
137.	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 Research 14, 2145-2154, 2004.
136.	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.
135.	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 Research 32, D217-D222, 2004.
134.	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.
133.	B. John, A. Sali. Detection of homologous proteins by an intermediate sequence search. Protein Science 13, 54-62, 2004.
132.	F. Alber, N. Eswar, A. Sali. Structure determination of macromolecular complexes by experiment and computation. Practical Bioinformatics, Ed: J.Bujnicki 15, 73-96, 2004.
131.	M.A. Marti-Renom, M.S. Madhusudhan, A. Sali. Alignment of protein sequences by their profiles. Protein Science 13, 1071-1087, 2004.
130.	A. Rossi, Q. Deveraux, B. Turk, A. Sali. Comprehensive search for cysteine cathepsins in the human genome. Biological Chemistry 385, 363-372, 2004.
129.	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 Research 64, 3790-3797, 2004.
128.	A. Fiser, A. Sali. ModLoop: automated modeling of loops in protein structures. Bioinformatics 19, 2500-2501, 2003.
127.	A. Sali. NIH workshop on structural proteomics of biological complexes. Structure 11, 1043-1047, 2003.
126.	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.
125.	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.
124.	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.
123.	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 Research 31, 3375-3380, 2003.
122.	B. John, A. Sali. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Research 31, 3982-3992, 2003.
121.	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 Research 31, 3311-3315, 2003.
120.	A. Sali, R. Glaeser, T. Earnest, W. Baumeister. From words to literature in structural proteomics. Nature 422, 216-225, 2003.
119.	A. Fiser, A. Sali. Comparative Protein Structure Modeling. In: Protein Structure. Ed: D. Chasman, pp. 167-206, Marcel Dekker, Inc., Oxford, UK, 2003.
118.	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.
117.	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.
116.	A. Fiser, A. Sali. Modeller: generation and refinement of homology-based protein structure models. Methods in Enzymology 374, 461-491, 2003.
115.	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. Journal of Immunology 169, 7097-7103, 2002.
114.	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.
113.	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. Journal of Biological Chemistry 277, 25756-25774, 2002.
112.	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.
111.	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 Science 11, 723-738, 2002.
110.	U. Pieper, N. Eswar, A.C. Stuart, V.A. Ilyin, A. Sali. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Research 30, 255-259, 2002.
109.	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.
108.	A. Sali, M.A. Marti-Renom, M.S. Madhusudhan, A. Fiser, B. Rost. Reply to Moult et al. Structure 10, 292-293, 2002.
107.	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.
106.	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.
105.	F. Melo, R. Sanchez, A. Sali. Statistical potentials for fold assessment. Protein Science 11, 430-448, 2002.
104.	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. Biochemical and Biophysical Research Communications 293, 633-639, 2002.
103.	D. Baker, A. Sali. Protein structure prediction and structural genomics. Science 294, 93-96, 2001.
102.	C.M. Groft, R. Beckmann, A. Sali, S.K. Burley. Response to Paoli. Nature Structural Biology 8, 745, 2001.
101.	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.
100.	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. Journal of Biological Chemistry 276, 49169-49182, 2001.
99.	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.
98.	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.
97.	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. Proceedings of the National Academy of Sciences of the United States of America 98, 12896-12901, 2001.
96.	A. Sali. Target practice. Nature Structural Biology 8, 482-484, 2001.
95.	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. Journal of Biomolecular NMR 19, 289-290, 2001.
94.	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. Journal of Biological Chemistry 276, 20648-20658, 2001.
93.	M.A. Marti-Renom, V.A. Ilyin, A. Sali. DBAli: a database of protein structure alignments. Bioinformatics 17, 746-747, 2001.
92.	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.
91.	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. Nature Genetics 27, 337-340, 2001.
90.	C.M. Groft, R. Beckmann, A. Sali, S.K. Burley. Crystal structures of ribosome anti-association factor IF6. Nature Structural Biology 7, 1156-1164, 2000.
89.	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.
88.	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. Nature Structural Biology 7, 986-990, 2000.
87.	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. Proceedings of the National Academy of Sciences of the United States of America 97, 7301-7306, 2000.
86.	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.
85.	A. Fiser, R.K.G. Do, A. Sali. Modeling of loops in protein structures. Protein Science 9, 1753-1773, 2000.
84.	G. Wu, A.G. McArthur, A. Fiser, A. Sali, M.L. Sogin, M. Muller. Core histones of the amitochondriate protist, Giardia lamblia. Molecular Biology and Evolution 17, 1156-1163, 2000.
83.	R. Sanchez, A. Sali. Comparative protein structure modeling. Introduction and practical examples with modeller. Methods in Molecular Biology 143, 97-129, 2000.
82.	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 in Biochemical Sciences 25, 331-339, 2000.
81.	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 Research 28, 250-253, 2000.
80.	M.A. Marti-Renom, A.C. Stuart, A. Fiser, R. Sanchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annual Review of Biophysics and Biomolecular Structure 29, 291-325, 2000.
79.	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. Journal of Biological Chemistry 275, 351-358, 2000.
78.	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.
77.	A. Sali. Functional links between proteins. Nature 402, 23, 25-26, 1999.
76.	A. Sali, J. Kuriyan. Challenges at the frontiers of structural biology (Reprinted from Trends in Biochemical Science, vol 12, Dec., 1999). Trends in Cell Biology 9, M20-M24, 1999.
75.	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. Nature Genetics 23, 151-157, 1999.
74.	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. Journal of Biological Chemistry 274, 30784-30793, 1999.
73.	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.
72.	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. Nature Structural Biology 6, 615-619, 1999.
71.	G. Wu, A. Fiser, B. ter Kuile, A. Sali, M. Muller. Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase. Proceedings of the National Academy of Sciences USA 96, 6285-6290, 1999.
70.	R. Sanchez, A. Sali. Comparative protein structure modeling in genomics. Journal of Computational Physics 151, 388-401, 1999.
69.	R. Sanchez, A. Sali. MODBASE: A database of comparative protein structure models. Bioinformatics 15, 1060-1061, 1999.
68.	A. Sali. 100,000 protein structures for the biologist. Nature Structural Biology 5, 1029-1032, 1998.
67.	R. Sanchez, A. Sali. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proceedings of the National Academy of Sciences USA 95, 13597-13602, 1998.
66.	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.
65.	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. Journal of Chemical Physics 108, 6466-6483, 1998.
64.	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.
63.	C. Huang, A. Sali, R.L. Stevens. Regulation and function of mast cell proteases in inflammation. Journal of Clinical Immunology 18, 169-183, 1998.
62.	C.M. Dobson, A. Sali, M. Karplus. Protein folding: A perspective from theory and experiment. Angewandte Chemie Int. Ed. 37, 868-893, 1998.
61.	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. Annals of the New York Academy of Sciences 815, 331-333, 1997.
60.	R. Sanchez, A.Ya. Badretdinov, E. Feyfant, A. Sali. Homology protein structure modeling. Transactions of the American Crystallographic Association 32, 81-91, 1997.
59.	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.
58.	R. Sanchez, A. Sali. Evaluation of comparative protein structure modeling by MODELLER-3. Proteins Suppl 1, 50-58, 1997.
57.	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. Journal of Biological Chemistry 272, 29158-29166, 1997.
56.	D. Koulich, M. Orlova, A. Malhotra, A. Sali, S.A. Darst, S. Borukhov. Domain organization of Escherichia coli transcript cleavage factors GreA and GreB. Journal of Biological Chemistry 272, 7201-7210, 1997.
55.	R. Sanchez, A. Sali. Advances in comparative protein-structure modelling. Current Opinion in Structural Biology 7, 206-214, 1997.
54.	R. Sanchez, A. Sali. Comparative protein modeling as an optimization problem. Journal of Molecular Structure (Theochem) 398, 489-496, 1997.
53.	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. Journal of Biological Chemistry 272, 31885-31893, 1997.
52.	M. Russel, N.A. Linderoth, A. Sali. Filamentous phage assembly: variation on a protein export theme. Gene 192, 23-32, 1997.
51.	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.
50.	A.R. Dinner, A. Sali, M. Karplus. The folding mechanism of larger model proteins: role of native structure. Proceedings of the National Academy of Sciences U S A 93, 8356-8361, 1996.
49.	L.Z. Xu, R. Sanchez, A. Sali, N. Heintz. Ligand specificity of brain lipid-binding protein. Journal of Biological Chemistry 271, 24711-24719, 1996.
48.	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.
47.	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. Journal of Immunology 157, 3744-3751, 1996.
46.	M. Karplus, A. Sali, E. Shakhnovich. Kinetics of protein folding. Nature 373, 664-665, 1995.
45.	A. Sali. Modeling mutations and homologous proteins. Current Opinion in Biotechnology 6, 437-451, 1995.
44.	A. Sali, L. Potterton, F. Yuan, H. van Vlijmen, M. Karplus. Evaluation of comparative protein modeling by MODELLER. Proteins 23, 318-326, 1995.
43.	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.
42.	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.
41.	A. Sali. Comparative protein modeling by satisfaction of spatial restraints. Molecular Medicine Today 1, 270-277, 1995.
40.	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. Journal of Biological Chemistry 270, 19524-19531, 1995.
39.	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.
38.	A. Sali. MODELLER: Implementing 3D protein modeling. In: mc^2, 2, pp. 5, Molecular Simulations Inc., Totowa, NJ, 1995.
37.	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.
36.	M. Karplus, A. Sali. Theoretical studies of protein folding and unfolding. Current Opinion in Structural Biology 5, 58-73, 1995.
35.	A. Dinner, A. Sali, M. Karplus, E. Shakhnovich. Phase diagram of a model protein derived by exhaustive enumeration of the conformations. Journal of Chemical Physics 101, 1444-1451, 1994.
34.	A. Sali, E. Shakhnovich, M. Karplus. How does a protein fold? Nature 369, 248-251, 1994.
33.	A. Sali, E. Shakhnovich, M. Karplus. Kinetics of protein folding. A lattice model study of the requirements for folding to the native state. Journal of Molecular Biology 235, 1614-1636, 1994.
32.	A. Sali, J.P. Overington. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Science 3, 1582-1596, 1994.
31.	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.
30.	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. Journal of Biological Chemistry 268, 9023-9034, 1993.
29.	A. Sali, T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology 234, 779-815, 1993.
28.	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. Biochemical Society Transactions 21 ( Pt 3), 597-604, 1993.
27.	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.
26.	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 Science 1, 216-226, 1992.
25.	Z.Y. Zhu, A. Sali, T.L. Blundell. A variable gap penalty function and feature weights for protein 3-D structure comparisons. Protein Engineering 5, 43-51, 1992.
24.	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 Science 1, 322-328, 1992. PMC2142209
23.	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.
22.	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.
21.	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.
20.	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. Advances in Experimental Medicine and Biology 306, 443-453, 1991.
19.	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.
18.	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.
17.	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.
16.	M.S. Johnson, A. Sali, T.L. Blundell. Phylogenetic relationships from three-dimensional protein structures. Methods in Enzymology 183, 670-690, 1990.
15.	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. Current Science 59, 867-874, 1990.
14.	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.
13.	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. Journal of Molecular Biology 216, 1017-1029, 1990.
12.	A. Sali, J.P. Overington, M.S. Johnson, T.L. Blundell. From Comparisons of protein sequences and structures to protein modelling and design. Trends in Biochemical Sciences 15, 235-240, 1990.
11.	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. Journal of Molecular Biology 212, 403-428, 1990.
10.	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.
9.	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.
8.	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.
7.	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.
6.	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.
5.	A. Sali, V. Turk. Prediction of the secondary structures of stefins and cystatins, the low-molecular mass protein inhibitors of cysteine proteinases. Biological Chemistry Hoppe-Seyler 368, 493-499, 1987.
4.	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.
3.	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.
2.	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.
1.	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.