UCSF Laboratory of Andrej Sali QB3

Publications

325.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, in press.
324.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. submitted.
323.B. Webb, A. Sali. Comparative protein structure modeling. In: submitted.
322.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. submitted.
321.J. Johnson, S. Santos, U. Pieper, A. Sali, N. Krogan, P. Beltrao. Conservation and structural analysis of the Xenopus laevis phospho-proteome. submitted.
320.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. PMCID3874021
319.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.
318.G. Clinthorne, M. Bonomi, R. Pellarin, K. Molnar, G. Gonzalez, S. Goldberg, A. Sali, W. DeGrado. PhoQ, a histidine kinase, signals across the membrane using a scissoring mechanism. submitted.
317.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. PMCID3965011
316.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. PMCID3902174
315.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. PMCID TBD by Journal
314.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. PMCID3813303
313.M. Kostic, C. Lima, A. Sali. Celebrating 20 Years of Structural Biology. Structure 21, 1477-1478, 2013. PMCID TBD by Journal
312.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. PMCID3789770
311.M. Bonomi, E.G. Muller, R. Pellarin, S.J. Kim, D. Russel, R. Ramsden, B.A. Sundin, T.A. Davis, A. Sali. Protein complex structures from Bayesian modeling of in vivo FRET data. submitted.
310.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. PMCID3842762
309.P. Weinkam, A. Sali. Mapping Polymerization and Allostery of Hemoglobin S Using Point Mutations. J Phys Chem B 117, 13058-13068, 2013. PMCID3973026
308.Y. Spill, S.J. Kim, D. Schneidman-Duhovny, D. Russel, B. Webb, A. Sali, M. Nilges. SAXS Merge: an automated webserver to statistically merge SAXS profiles. submitted.
307.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. PMCID3767544
306.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. PMCID38227683
305.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.
304.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. PMCID3752106
303.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. PMCID TBD by Journal
302.A. Schlessinger, S.W. Yee, A. Sali, K. Giacomini. SLC classification: an update. Clin Pharmacol Ther 94, 19-23, 2013. PMCID TBD by Journal
301.B. Webb, A. Sali. Protein structure modeling with MODELLER. In: Methods in Molecular Biology, in press, Humana Press, 2013.
300.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. PMCID3619328
299.A. Ward, A. Sali, I. Wilson. Integrative structural biology. Science 339, 913-915, 2013. PMCID3633482
298.P. Weinkam, Y.C. Chen, J. Pons, A. Sali. Impact of mutations on the allosteric conformational equilibrium. J Mol Biol 425, 647-661, 2013. PMCID3557769
297.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. PMCID3840220
296.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. PMCID3702627
295.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. PMCID3637775
294.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. PMCID TBD by Journal
293.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. PMCID3678552
292.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. PMCID3661711
291.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. PMCID3755625
290.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. PMCID3645303
289.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. PMCID TBD by Journal
288.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. PMCID3557803
287.D. Schneidman-Duhovny, S.J. Kim, A. Sali. Integrative structural modeling with small angle X-ray scattering profiles. BMC Struct Biol 12, 17, 2012. PMCID3427135
286.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. PMCID3488050
285.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. PMCID3503826
284.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. PMCID3503186
283.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. PMCID3496023
282.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. PMCID3412957
281.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. PMCID3420364
280.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. PMCID3400954
279.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. PMCID TBD by Journal
278.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. PMCID TBD by Journal
277.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. PMCID3519461
276.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. PMCID3723349
275.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. PMCID3686472
274.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. PMCID3277140
273.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. PMCID3252951
272.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. PMCID3260315
271.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. PMCID3324024
270.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. PMCID3328769
269.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. PMCID3283990
268.H. Fan, J. Irwin, A. Sali. Virtual Ligand Screening Against Comparative Protein Structure Models. Methods Mol Biol 819, 105-126, 2012. PMCID3386294
267.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, pp. 331-350, Humana Press, New York, NY, 2012.
266.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. PMCID3238057
265.A.M. Goble, H. Fan, A. Sali, F.M. Raushel. Discovery of a Cytokinin Deaminase. ACS Chem Biol 6, 1036-1040, 2011. PMCID3199332
264.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. PMCID3410985
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. PMCID3329222
262.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. PMCID3179104
261.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. PMCID3197762
260.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. PMCID3125811
259.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. PMCID3310910
258.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. PMCID3310911
257.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. PMCID3246566
256.M. Field, A. Sali, M. Rout. On a bender: Bars, ESCRTs, COPs, and finally getting your coat. J Cell Biol 193, 963-972, 2011. PMCID3115789
255.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 10, M110.006478, 2011. PMCID3108837
254.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. PMCID3043370
253.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. PMCID3350809
252.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.
251.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 50, 1917-1927, 2011. PMCID3059353
250.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. PMCID3013688
249.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.
248.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. PMCID3040266
247.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. PMCID2938054
246.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. PMCID3005782
245.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. PMCID2957788
244.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. PMCID2952722
243.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. PMCID2989796
242.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. PMCID3136511
241.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. PMCID2938050
240.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. PMCID2896111
239.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. PMCID2866268
238.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. PMCID2976715
237.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. PMCID2906887
236.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. PMCID2894511
235.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. PMCID2816688
234.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. PMCID2923222
233.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. PMCID2771176
232.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. PMCID2790034
231.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. PMCID2814252
230.T. Lezon, A. Sali, I. Bahar. Global motions of the nuclear pore complex:Insights from Elastic Network Models. PLoS Comp Biol 5, e1000496, 2009. PMCID2725293
229.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. PMCID2780624
228.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. PMCID2742445
227.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. PMCID2909824
226.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. PMCID2680734
225.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. PMCID2715492
224.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. PMCID2687990
223.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. PMCID3088649
222.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. PMCID2705707
221.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. PMCID2682653
220.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. PMCID2667270
219.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. PMCID2739730
218.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. PMCID2774249
217.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. PMCID2774440
216.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. PMCID2659619
215.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. PMCID2756966
214.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. PMCID2686492
213.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. PMCID2693957
212.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.
211.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. PMCID3178102
210.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. PMCID2474495
209.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. PMCID2566540
208.R.A. Chiang, A. Sali, P.C. Babbitt. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol 4, e1000142, 2008. PMCID2453236
207.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. PMCID2279195
206.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. PMCID2745287
205.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. PMCID2578807
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. PMCID2600884
203.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. PMCID2587343
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. Nat Rev Drug Discov 7, 900-907, 2008. PMCID3184002
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. PMCID2430716
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. PMCID2409374
199.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.
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. PMCID2775484
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. Nat Struct Mol Biol 15, 746-753, 2008. PMCID2546500
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. J Mol Biol 375, 331-336, 2008. PMCID2680129
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 Mol Biol 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.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.
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 Sci 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. J Struct Funct Genom 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 Sci 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 Res 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 Comput Biol 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 Comput Biol 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 Sci 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 Res 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. Pac Symp Biocomput, 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.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.
171.M.Y. Shen, A. Sali. Statistical potential for assessment and prediction of protein structures. Protein Sci 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. J Mol Biol 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. Pharmacol Rev 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 Res 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 Sci 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 Sci 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. J Mol Biol 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 Res 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. Proc Natl Acad Sci 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. Curr Opin Struct Biol 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. J Struct Funct Genom 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. Chem Phys Lett 405, 224-228, 2005.
152.D. Korkin, F.P. Davis, A. Sali. Localization of protein-binding sites within families of proteins. Protein Sci 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. Pac Symp Biocomput, 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. J Struct Biol 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. Proc Natl Acad Sci 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. Curr Opin Struct Biol 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 Res 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, 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 Res 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 Sci 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 Sci 13, 1071-1087, 2004.
130.A. Rossi, Q. Deveraux, B. Turk, A. Sali. Comprehensive search for cysteine cathepsins in the human genome. Biol Chem 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 Res 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., 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 Res 31, 3375-3380, 2003.
122.B. John, A. Sali. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res 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 Res 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., 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, 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 Enzymol 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. J Immunol 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, 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. J Biol Chem 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 Sci 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 Res 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 Sci 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. Biochem Biophys Res Commun 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. Nat Struct Biol 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. J Biol Chem 276, 49169-49182, 2001.
99.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. .
99.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. .
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. Proc Natl Acad Sci U S A 98, 12896-12901, 2001.
96.A. Sali. Target practice. Nat Struct Biol 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. J Biomol 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. J Biol Chem 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. Nat Genet 27, 337-340, 2001.
90.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.
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, 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. Nat Struct Biol 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. Proc Natl Acad Sci U S A 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 Sci 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. Mol Biol Evol 17, 1156-1163, 2000.
83.R. Sanchez, A. Sali. Comparative protein structure modeling. Introduction and practical examples with modeller. Methods Mol Biol 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 Biochem Sci 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 Res 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. Annu Rev Biophys Biomol Struct 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. J Biol Chem 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 Cell Biol 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. Nat Genet 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. J Biol Chem 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. Nat Struct Biol 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. Proc Natl Acad Sci U S A 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. Nat Struct Biol 5, 1029-1032, 1998.
67.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.
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. J Chem Phys 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. J Clin Immunol 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. Ann N Y Acad Sci 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. J Biol Chem 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. J Biol Chem 272, 7201-7210, 1997.
55.R. Sanchez, A. Sali. Advances in comparative protein-structure modelling. Curr Opin Struct Biol 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. J Biol Chem 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. Proc Natl Acad Sci U S A 93, 8356-8361, 1996.
49.L.Z. Xu, R. Sanchez, A. Sali, N. Heintz. Ligand specificity of brain lipid-binding protein. J Biol Chem 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. J Immunol 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. Curr Opin Biotechnol 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, 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., 1995.
41.A. Sali. Comparative protein modeling by satisfaction of spatial restraints. Mol Med 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. J Biol Chem 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., 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, 1995.
36.M. Karplus, A. Sali. Theoretical studies of protein folding and unfolding. Curr Opin Struct Biol 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. J Chem Phys 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. J Mol Biol 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 Sci 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. J Biol Chem 268, 9023-9034, 1993.
29.A. Sali, T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 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. Biochem Soc Trans 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, 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 Sci 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 Eng 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 Sci 1, 322-328, 1992.
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., 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. Adv Exp Med Biol 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., 1990.
16.M.S. Johnson, A. Sali, T.L. Blundell. Phylogenetic relationships from three-dimensional protein structures. Methods Enzymol 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. Curr Sci 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. J Mol Biol 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 Biochem Sci 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. J Mol Biol 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, 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, 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. Biol Chem 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.
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 94158-2330, Tel +1 (415) 514-4227, Fax +1 (415) 514-4231, 4234, , Web http://www.salilab.org, Assistant: Ms. Hilary Mahon, Email: , Tel +1 (415) 514-4228, Lab +1 (415) 514-4258, 4233