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    Andrej Sali, PhD

    TitleProfessor
    SchoolUCSF School of Pharmacy
    DepartmentBioengineering and Therapeutic Sciences
    Address1700 4th Street, Byers Hall
    San Francisco CA 94143
    Phone415-514-4227

       Overview 
       Overview
      We are using computation grounded in the laws of physics and evolution to study the structure and function of proteins. We aim to improve and apply methods for: (i) )predicting the structures of proteins; (ii) determining the structures of macromolecular assemblies; (iii) annotating the functions of proteins using their structures. This research enhances the impact of genome sequencing, structural genomics, and functional genomics on biology and medicine.


       Bibliographic 
       Publications
      Publications by year:
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
      1. van Dam TJ, Townsend MJ, Turk M, Schlessinger A, Sali A, Field MC, Huynen MA. Evolution of modular intraflagellar transport from a coatomer-like progenitor. Proc Natl Acad Sci U S A. 2013 Apr 23; 110(17):6943-8.
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      2. Pedersen BP, Kumar H, Waight AB, Risenmay AJ, Roe-Zurz Z, Chau BH, Schlessinger A, Bonomi M, Harries W, Sali A, Johri AK, Stroud RM. Crystal structure of a eukaryotic phosphate transporter. Nature. 2013 Apr 25; 496(7446):533-6.
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      3. Geier EG, Schlessinger A, Fan H, Gable JE, Irwin JJ, Sali A, Giacomini KM. Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1. Proc Natl Acad Sci U S A. 2013 Apr 2; 110(14):5480-5.
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      4. Sampathkumar P, Kim SJ, Upla P, Rice WJ, Phillips J, Timney BL, Pieper U, Bonanno JB, Fernandez-Martinez J, Hakhverdyan Z, Ketaren NE, Matsui T, Weiss TM, Stokes DL, Sauder JM, Burley SK, Sali A, Rout MP, Almo SC. Structure, dynamics, evolution, and function of a major scaffold component in the nuclear pore complex. Structure. 2013 Apr 2; 21(4):560-71.
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      5. Guttman M, Weinkam P, Sali A, Lee KK. All-atom ensemble modeling to analyze small-angle x-ray scattering of glycosylated proteins. Structure. 2013 Mar 5; 21(3):321-31.
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      6. Ward AB, Sali A, Wilson IA. Biochemistry. Integrative structural biology. Science. 2013 Feb 22; 339(6122):913-5.
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      7. Pieper U, Schlessinger A, Kloppmann E, Chang GA, Chou JJ, Dumont ME, Fox BG, Fromme P, Hendrickson WA, Malkowski MG, Rees DC, Stokes DL, Stowell MH, Wiener MC, Rost B, Stroud RM, Stevens RC, Sali A. Coordinating the impact of structural genomics on the human a-helical transmembrane proteome. Nat Struct Mol Biol. 2013 Feb; 20(2):135-8.
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      8. Wittwer MB, Zur AA, Khuri N, Kido Y, Kosaka A, Zhang X, Morrissey KM, Sali A, Huang Y, Giacomini KM. Discovery of Potent, Selective Multidrug and Toxin Extrusion Transporter 1 (MATE1, SLC47A1) Inhibitors Through Prescription Drug Profiling and Computational Modeling. J Med Chem. 2013 Feb 14; 56(3):781-95.
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      9. Fan H, Hitchcock DS, Seidel RD, Hillerich B, Lin H, Almo SC, Sali A, Shoichet BK, Raushel FM. Assignment of pterin deaminase activity to an enzyme of unknown function guided by homology modeling and docking. J Am Chem Soc. 2013 Jan 16; 135(2):795-803.
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      10. Weinkam P, Chen YC, Pons J, Sali A. Impact of mutations on the allosteric conformational equilibrium. J Mol Biol. 2013 Feb 8; 425(3):647-61.
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      11. Kolb P, Phan K, Gao ZG, Marko AC, Sali A, Jacobson KA. Limits of ligand selectivity from docking to models: in silico screening for a(1) adenosine receptor antagonists. PLoS One. 2012; 7(11):e49910.
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      12. Velázquez-Muriel J, Lasker K, Russel D, Phillips J, Webb BM, Schneidman-Duhovny D, Sali A. Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images. Proc Natl Acad Sci U S A. 2012 Nov 13; 109(46):18821-6.
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      13. Schneidman-Duhovny D, Rossi A, Avila-Sakar A, Kim SJ, Velázquez-Muriel J, Strop P, Liang H, Krukenberg KA, Liao M, Kim HM, Sobhanifar S, Dötsch V, Rajpal A, Pons J, Agard DA, Cheng Y, Sali A. A method for integrative structure determination of protein-protein complexes. Bioinformatics. 2012 Dec 1; 28(24):3282-9.
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      14. Martinez-Avila O, Wu S, Kim SJ, Cheng Y, Khan F, Samudrala R, Sali A, Horst JA, Habelitz S. Self-Assembly of Filamentous Amelogenin Requires Calcium and Phosphate: From Dimers via Nanoribbons to Fibrils. Biomacromolecules. 2012 Nov 12; 13(11):3494-502.
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      15. Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JD. Strategic protein target analysis for developing drugs to stop dental caries. Adv Dent Res. 2012 Sep; 24(2):86-93.
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      16. Markley JL, Akutsu H, Asakura T, Baldus M, Boelens R, Bonvin A, Kaptein R, Bax A, Bezsonova I, Gryk MR, Hoch JC, Korzhnev DM, Maciejewski MW, Case D, Chazin WJ, Cross TA, Dames S, Kessler H, Lange O, Madl T, Reif B, Sattler M, Eliezer D, Fersht A, Forman-Kay J, Kay LE, Fraser J, Gross J, Kortemme T, Sali A, Fujiwara T, Gardner K, Luo X, Rizo-Rey J, Rosen M, Gil RR, Ho C, Rule G, Gronenborn AM, Ishima R, Klein-Seetharaman J, Tang P, van der Wel P, Xu Y, Grzesiek S, Hiller S, Seelig J, Laue ED, Mott H, Nietlispach D, Barsukov I, Lian LY, Middleton D, Blumenschein T, Moore G, Campbell I, Schnell J, Vakonakis IJ, Watts A, Conte MR, Mason J, Pfuhl M, Sanderson MR, Craven J, Williamson M, Dominguez C, Roberts G, Günther U, Overduin M, Werner J, Williamson P, Blindauer C, Crump M, Driscoll P, Frenkiel T, Golovanov A, Matthews S, Parkinson J, Uhrin D, Williams M, Neuhaus D, Oschkinat H, Ramos A, Shaw DE, Steinbeck C, Vendruscolo M, Vuister GW, Walters KJ, Weinstein H, Wüthrich K, Yokoyama S. In support of the BMRB. Nat Struct Mol Biol. 2012 Sep; 19(9):854-60.
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      17. Schlessinger A, Wittwer MB, Dahlin A, Khuri N, Bonomi M, Fan H, Giacomini KM, Sali A. High Selectivity of the ?-Aminobutyric Acid Transporter 2 (GAT-2, SLC6A13) Revealed by Structure-based Approach. J Biol Chem. 2012 Nov 2; 287(45):37745-56.
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      18. Schneidman-Duhovny D, Kim SJ, Sali A. Integrative structural modeling with small angle X-ray scattering profiles. BMC Struct Biol. 2012; 12:17.
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      19. Sampathkumar P, Kim SJ, Manglicmot D, Bain KT, Gilmore J, Gheyi T, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Matsui T, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Almo SC, Burley SK. Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata. Proteins. 2012 Aug; 80(8):2110-6.
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      20. Trinidad JC, Barkan DT, Gulledge BF, Thalhammer A, Sali A, Schoepfer R, Burlingame AL. Global identification and characterization of both O-GlcNAcylation and phosphorylation at the murine synapse. Mol Cell Proteomics. 2012 Aug; 11(8):215-29.
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      21. Braberg H, Webb BM, Tjioe E, Pieper U, Sali A, Madhusudhan MS. SALIGN: a web server for alignment of multiple protein sequences and structures. Bioinformatics. 2012 Aug 1; 28(15):2072-3.
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      22. Klammt C, Maslennikov I, Bayrhuber M, Eichmann C, Vajpai N, Chiu EJ, Blain KY, Esquivies L, Kwon JH, Balana B, Pieper U, Sali A, Slesinger PA, Kwiatkowski W, Riek R, Choe S. Facile backbone structure determination of human membrane proteins by NMR spectroscopy. Nat Methods. 2012 Aug; 9(8):834-9.
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      23. Weinkam P, Pons J, Sali A. Structure-based model of allostery predicts coupling between distant sites. Proc Natl Acad Sci U S A. 2012 Mar 27; 109(13):4875-80.
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      24. Puizdar V, Zajc T, Zerovnik E, Renko M, Pieper U, Eswar N, Sali A, Dolenc I, Turk V. Biochemical characterization and structural modeling of human cathepsin E variant 2 in comparison to the wild-type protein. Biol Chem. 2012 Mar; 393(3):177-86.
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      25. Fernandez-Martinez J, Phillips J, Sekedat MD, Diaz-Avalos R, Velazquez-Muriel J, Franke JD, Williams R, Stokes DL, Chait BT, Sali A, Rout MP. Structure-function mapping of a heptameric module in the nuclear pore complex. J Cell Biol. 2012 Feb 20; 196(4):419-34.
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      26. Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing KH, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL. Outcome of the first electron microscopy validation task force meeting. Structure. 2012 Feb 8; 20(2):205-14.
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      27. Lasker K, Förster F, Bohn S, Walzthoeni T, Villa E, Unverdorben P, Beck F, Aebersold R, Sali A, Baumeister W. Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach. Proc Natl Acad Sci U S A. 2012 Jan 31; 109(5):1380-7.
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      28. Russel D, Lasker K, Webb B, Velázquez-Muriel J, Tjioe E, Schneidman-Duhovny D, Peterson B, Sali A. Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol. 2012 Jan; 10(1):e1001244.
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      29. Fan H, Irwin JJ, Sali A. Virtual ligand screening against comparative protein structure models. Methods Mol Biol. 2012; 819:105-26.
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      30. Lasker K, Velázquez-Muriel JA, Webb BM, Yang Z, Ferrin TE, Sali A. Macromolecular assembly structures by comparative modeling and electron microscopy. Methods Mol Biol. 2012; 857:331-50.
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      31. Jäger S, Kim DY, Hultquist JF, Shindo K, LaRue RS, Kwon E, Li M, Anderson BD, Yen L, Stanley D, Mahon C, Kane J, Franks-Skiba K, Cimermancic P, Burlingame A, Sali A, Craik CS, Harris RS, Gross JD, Krogan NJ. Vif hijacks CBF-ß to degrade APOBEC3G and promote HIV-1 infection. Nature. 2012 Jan 19; 481(7381):371-5.
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      32. Jäger S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. Global landscape of HIV-human protein complexes. Nature. 2012 Jan 19; 481(7381):365-70.
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      33. Pathare GR, Nagy I, Bohn S, Unverdorben P, Hubert A, Körner R, Nickell S, Lasker K, Sali A, Tamura T, Nishioka T, Förster F, Baumeister W, Bracher A. The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together. Proc Natl Acad Sci U S A. 2012 Jan 3; 109(1):149-54.
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      34. Fan H, Schneidman-Duhovny D, Irwin JJ, Dong G, Shoichet BK, Sali A. Statistical potential for modeling and ranking of protein-ligand interactions. J Chem Inf Model. 2011 Dec 27; 51(12):3078-92.
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      35. Gerlt JA, Allen KN, Almo SC, Armstrong RN, Babbitt PC, Cronan JE, Dunaway-Mariano D, Imker HJ, Jacobson MP, Minor W, Poulter CD, Raushel FM, Sali A, Shoichet BK, Sweedler JV. The Enzyme Function Initiative. Biochemistry. 2011 Nov 22; 50(46):9950-62.
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      36. Lima C, Sali A, Kostic M. Structure meets the membrane. Structure. 2011 Oct 12; 19(10):1347.
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      37. Yang Z, Lasker K, Schneidman-Duhovny D, Webb B, Huang CC, Pettersen EF, Goddard TD, Meng EC, Sali A, Ferrin TE. UCSF Chimera, MODELLER, and IMP: an integrated modeling system. J Struct Biol. 2012 Sep; 179(3):269-78.
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      38. Carlsson J, Coleman RG, Setola V, Irwin JJ, Fan H, Schlessinger A, Sali A, Roth BL, Shoichet BK. Ligand discovery from a dopamine D3 receptor homology model and crystal structure. Nat Chem Biol. 2011 Nov; 7(11):769-78.
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      39. Schlessinger A, Geier E, Fan H, Irwin JJ, Shoichet BK, Giacomini KM, Sali A. Structure-based discovery of prescription drugs that interact with the norepinephrine transporter, NET. Proc Natl Acad Sci U S A. 2011 Sep 20; 108(38):15810-5.
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      40. Goble AM, Fan H, Sali A, Raushel FM. Discovery of a cytokinin deaminase. ACS Chem Biol. 2011 Oct 21; 6(10):1036-40.
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      41. Tjioe E, Lasker K, Webb B, Wolfson HJ, Sali A. MultiFit: a web server for fitting multiple protein structures into their electron microscopy density map. Nucleic Acids Res. 2011 Jul; 39(Web Server issue):W167-70.
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      42. Field MC, Sali A, Rout MP. Evolution: On a bender--BARs, ESCRTs, COPs, and finally getting your coat. J Cell Biol. 2011 Jun 13; 193(6):963-72.
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      43. Dokudovskaya S, Waharte F, Schlessinger A, Pieper U, Devos DP, Cristea IM, Williams R, Salamero J, Chait BT, Sali A, Field MC, Rout MP, Dargemont C. A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Mol Cell Proteomics. 2011 Jun; 10(6):M110.006478.
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      44. Sampathkumar P, Gheyi T, Miller SA, Bain KT, Dickey M, Bonanno JB, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sali A, Sauder JM, Burley SK. Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex. Proteins. 2011 May; 79(5):1672-7.
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      45. Kamat SS, Bagaria A, Kumaran D, Holmes-Hampton GP, Fan H, Sali A, Sauder JM, Burley SK, Lindahl PA, Swaminathan S, Raushel FM. Catalytic mechanism and three-dimensional structure of adenine deaminase. Biochemistry. 2011 Mar 22; 50(11):1917-27.
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      46. Kamat SS, Fan H, Sauder JM, Burley SK, Shoichet BK, Sali A, Raushel FM. Enzymatic deamination of the epigenetic base N-6-methyladenine. J Am Chem Soc. 2011 Feb 23; 133(7):2080-3.
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      47. Webb B, Lasker K, Schneidman-Duhovny D, Tjioe E, Phillips J, Kim SJ, Velázquez-Muriel J, Russel D, Sali A. Modeling of proteins and their assemblies with the integrative modeling platform. Methods Mol Biol. 2011; 781:377-97.
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      48. Pieper U, Webb BM, Barkan DT, Schneidman-Duhovny D, Schlessinger A, Braberg H, Yang Z, Meng EC, Pettersen EF, Huang CC, Datta RS, Sampathkumar P, Madhusudhan MS, Sjölander K, Ferrin TE, Burley SK, Sali A. ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2011 Jan; 39(Database issue):D465-74.
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      49. Lasker K, Sali A, Wolfson HJ. Determining macromolecular assembly structures by molecular docking and fitting into an electron density map. Proteins. 2010 Nov 15; 78(15):3205-11.
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      50. Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A. Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains. Protein Sci. 2010 Nov; 19(11):2110-21.
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      51. Chen L, Pawlikowski B, Schlessinger A, More SS, Stryke D, Johns SJ, Portman MA, Chen E, Ferrin TE, Sali A, Giacomini KM. Role of organic cation transporter 3 (SLC22A3) and its missense variants in the pharmacologic action of metformin. Pharmacogenet Genomics. 2010 Nov; 20(11):687-99.
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      52. Sampathkumar P, Lu F, Zhao X, Li Z, Gilmore J, Bain K, Rutter ME, Gheyi T, Schwinn KD, Bonanno JB, Pieper U, Fajardo JE, Fiser A, Almo SC, Swaminathan S, Chance MR, Baker D, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Sali A, Sauder JM, Burley SK. Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 A resolution. Proteins. 2010 Nov 1; 78(14):3056-62.
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      53. Schneidman-Duhovny D, Hammel M, Sali A. Macromolecular docking restrained by a small angle X-ray scattering profile. J Struct Biol. 2011 Mar; 173(3):461-71.
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      54. Sampathkumar P, Ozyurt SA, Do J, Bain KT, Dickey M, Rodgers LA, Gheyi T, Sali A, Kim SJ, Phillips J, Pieper U, Fernandez-Martinez J, Franke JD, Martel A, Tsuruta H, Atwell S, Thompson DA, Emtage JS, Wasserman SR, Rout MP, Sauder JM, Burley SK. Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup145. Proteins. 2010 Jun; 78(8):1992-8.
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      55. Schneidman-Duhovny D, Hammel M, Sali A. FoXS: a web server for rapid computation and fitting of SAXS profiles. Nucleic Acids Res. 2010 Jul; 38(Web Server issue):W540-4.
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      56. Lasker K, Phillips JL, Russel D, Velázquez-Muriel J, Schneidman-Duhovny D, Tjioe E, Webb B, Schlessinger A, Sali A. Integrative structure modeling of macromolecular assemblies from proteomics data. Mol Cell Proteomics. 2010 Aug; 9(8):1689-702.
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      57. Barkan DT, Hostetter DR, Mahrus S, Pieper U, Wells JA, Craik CS, Sali A. Prediction of protease substrates using sequence and structure features. Bioinformatics. 2010 Jul 15; 26(14):1714-22.
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      58. Förster F, Lasker K, Nickell S, Sali A, Baumeister W. Toward an integrated structural model of the 26S proteasome. Mol Cell Proteomics. 2010 Aug; 9(8):1666-77.
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      59. Gruswitz F, Chaudhary S, Ho JD, Schlessinger A, Pezeshki B, Ho CM, Sali A, Westhoff CM, Stroud RM. Function of human Rh based on structure of RhCG at 2.1 A. Proc Natl Acad Sci U S A. 2010 May 25; 107(21):9638-43.
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      60. Schlessinger A, Matsson P, Shima JE, Pieper U, Yee SW, Kelly L, Apeltsin L, Stroud RM, Ferrin TE, Giacomini KM, Sali A. Comparison of human solute carriers. Protein Sci. 2010 Mar; 19(3):412-28.
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      61. Davis FP, Sali A. The overlap of small molecule and protein binding sites within families of protein structures. PLoS Comput Biol. 2010 Feb; 6(2):e1000668.
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      62. Taylor DJ, Devkota B, Huang AD, Topf M, Narayanan E, Sali A, Harvey SC, Frank J. Comprehensive molecular structure of the eukaryotic ribosome. Structure. 2009 Dec 9; 17(12):1591-604.
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      63. Fan H, Irwin JJ, Webb BM, Klebe G, Shoichet BK, Sali A. Molecular docking screens using comparative models of proteins. J Chem Inf Model. 2009 Nov; 49(11):2512-27.
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      64. Kroetz DL, Ahituv N, Burchard EG, Guo S, Sali A, Giacomini KM. Institutional Profile: The University of California Pharmacogenomics Center: at the interface of genomics, biological mechanisms and drug therapy. Pharmacogenomics. 2009 Oct; 10(10):1569-76.
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      65. Kelly L, Pieper U, Eswar N, Hays FA, Li M, Roe-Zurz Z, Kroetz DL, Giacomini KM, Stroud RM, Sali A. A survey of integral alpha-helical membrane proteins. J Struct Funct Genomics. 2009 Dec; 10(4):269-80.
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      66. Lezon TR, Sali A, Bahar I. Global motions of the nuclear pore complex: insights from elastic network models. PLoS Comput Biol. 2009 Sep; 5(9):e1000496.
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      67. Förster F, Lasker K, Beck F, Nickell S, Sali A, Baumeister W. An atomic model AAA-ATPase/20S core particle sub-complex of the 26S proteasome. Biochem Biophys Res Commun. 2009 Oct 16; 388(2):228-33.
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      68. Madhusudhan MS, Webb BM, Marti-Renom MA, Eswar N, Sali A. Alignment of multiple protein structures based on sequence and structure features. Protein Eng Des Sel. 2009 Sep; 22(9):569-74.
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      69. Nickell S, Beck F, Scheres SH, Korinek A, Förster F, Lasker K, Mihalache O, Sun N, Nagy I, Sali A, Plitzko JM, Carazo JM, Mann M, Baumeister W. Insights into the molecular architecture of the 26S proteasome. Proc Natl Acad Sci U S A. 2009 Jul 21; 106(29):11943-7.
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      70. DeGrasse JA, DuBois KN, Devos D, Siegel TN, Sali A, Field MC, Rout MP, Chait BT. Evidence for a shared nuclear pore complex architecture that is conserved from the last common eukaryotic ancestor. Mol Cell Proteomics. 2009 Sep; 8(9):2119-30.
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      71. Peterson ME, Chen F, Saven JG, Roos DS, Babbitt PC, Sali A. Evolutionary constraints on structural similarity in orthologs and paralogs. Protein Sci. 2009 Jun; 18(6):1306-15.
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      72. Pandey KC, Barkan DT, Sali A, Rosenthal PJ. Regulatory elements within the prodomain of Falcipain-2, a cysteine protease of the malaria parasite Plasmodium falciparum. PLoS One. 2009; 4(5):e5694.
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      73. Ortí L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, Marti-Renom MA. A kernel for open source drug discovery in tropical diseases. PLoS Negl Trop Dis. 2009; 3(4):e418.
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      74. Fornes O, Aragues R, Espadaler J, Marti-Renom MA, Sali A, Oliva B. ModLink+: improving fold recognition by using protein-protein interactions. Bioinformatics. 2009 Jun 15; 25(12):1506-12.
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      75. Ortí L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, Marti-Renom MA. A kernel for the Tropical Disease Initiative. Nat Biotechnol. 2009 Apr; 27(4):320-1.
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      76. Lasker K, Topf M, Sali A, Wolfson HJ. Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly. J Mol Biol. 2009 Apr 24; 388(1):180-94.
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      77. Pieper U, Chiang R, Seffernick JJ, Brown SD, Glasner ME, Kelly L, Eswar N, Sauder JM, Bonanno JB, Swaminathan S, Burley SK, Zheng X, Chance MR, Almo SC, Gerlt JA, Raushel FM, Jacobson MP, Babbitt PC, Sali A. Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies. J Struct Funct Genomics. 2009 Apr; 10(2):107-25.
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      78. Russel D, Lasker K, Phillips J, Schneidman-Duhovny D, Velázquez-Muriel JA, Sali A. The structural dynamics of macromolecular processes. Curr Opin Cell Biol. 2009 Feb; 21(1):97-108.
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      79. Schwede T, Sali A, Honig B, Levitt M, Berman HM, Jones D, Brenner SE, Burley SK, Das R, Dokholyan NV, Dunbrack RL, Fidelis K, Fiser A, Godzik A, Huang YJ, Humblet C, Jacobson MP, Joachimiak A, Krystek SR, Kortemme T, Kryshtafovych A, Montelione GT, Moult J, Murray D, Sanchez R, Sosnick TR, Standley DM, Stouch T, Vajda S, Vasquez M, Westbrook JD, Wilson IA. Outcome of a workshop on applications of protein models in biomedical research. Structure. 2009 Feb 13; 17(2):151-9.
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      80. Stroud RM, Choe S, Holton J, Kaback HR, Kwiatkowski W, Minor DL, Riek R, Sali A, Stahlberg H, Harries W. 2007 annual progress report synopsis of the Center for Structures of Membrane Proteins. J Struct Funct Genomics. 2009 Apr; 10(2):193-208.
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      81. Li M, Hays FA, Roe-Zurz Z, Vuong L, Kelly L, Ho CM, Robbins RM, Pieper U, O'Connell JD, Miercke LJ, Giacomini KM, Sali A, Stroud RM. Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening. J Mol Biol. 2009 Jan 23; 385(3):820-30.
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      82. Hays FA, Roe-Zurz Z, Li M, Kelly L, Gruswitz F, Sali A, Stroud RM. Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination. J Struct Funct Genomics. 2009 Mar; 10(1):9-16.
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      83. Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A. MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2009 Jan; 37(Database issue):D347-54.
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      84. Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS, Campbell RK, Carmona S, Carruthers IM, Chan AW, Chen F, Crowther GJ, Doyle MA, Hertz-Fowler C, Hopkins AL, McAllister G, Nwaka S, Overington JP, Pain A, Paolini GV, Pieper U, Ralph SA, Riechers A, Roos DS, Sali A, Shanmugam D, Suzuki T, Van Voorhis WC, Verlinde CL. Genomic-scale prioritization of drug targets: the TDR Targets database. Nat Rev Drug Discov. 2008 Nov; 7(11):900-7.
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      85. Eramian D, Eswar N, Shen MY, Sali A. How well can the accuracy of comparative protein structure models be predicted? Protein Sci. 2008 Nov; 17(11):1881-93.
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      86. Mahrus S, Trinidad JC, Barkan DT, Sali A, Burlingame AL, Wells JA. Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell. 2008 Sep 5; 134(5):866-76.
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      87. Chiang RA, Sali A, Babbitt PC. Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol. 2008; 4(8):e1000142.
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      88. Förster F, Webb B, Krukenberg KA, Tsuruta H, Agard DA, Sali A. Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies. J Mol Biol. 2008 Oct 17; 382(4):1089-106.
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      89. Serysheva II, Ludtke SJ, Baker ML, Cong Y, Topf M, Eramian D, Sali A, Hamilton SL, Chiu W. Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel. Proc Natl Acad Sci U S A. 2008 Jul 15; 105(28):9610-5.
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      90. Booth CR, Meyer AS, Cong Y, Topf M, Sali A, Ludtke SJ, Chiu W, Frydman J. Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT. Nat Struct Mol Biol. 2008 Jul; 15(7):746-53.
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      91. Espadaler J, Eswar N, Querol E, Avilés FX, Sali A, Marti-Renom MA, Oliva B. Prediction of enzyme function by combining sequence similarity and protein interactions. BMC Bioinformatics. 2008; 9:249.
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      92. Krukenberg KA, Förster F, Rice LM, Sali A, Agard DA. Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90. Structure. 2008 May; 16(5):755-65.
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      93. Karchin R, Agarwal M, Sali A, Couch F, Beattie MS. Classifying Variants of Undetermined Significance in BRCA2 with protein likelihood ratios. Cancer Inform. 2008; 6:203-16.
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      94. Chandramouli P, Topf M, Ménétret JF, Eswar N, Cannone JJ, Gutell RR, Sali A, Akey CW. Structure of the mammalian 80S ribosome at 8.7 A resolution. Structure. 2008 Apr; 16(4):535-48.
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      95. Anderson CM, Korkin D, Smith DL, Makovets S, Seidel JJ, Sali A, Blackburn EH. Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break. Genes Dev. 2008 Apr 1; 22(7):854-9.
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      96. Topf M, Lasker K, Webb B, Wolfson H, Chiu W, Sali A. Protein structure fitting and refinement guided by cryo-EM density. Structure. 2008 Feb; 16(2):295-307.
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      97. Protein production and purification. Nat Methods. 2008 Feb; 5(2):135-46.
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      98. Eswar N, Eramian D, Webb B, Shen MY, Sali A. Protein structure modeling with MODELLER. Methods Mol Biol. 2008; 426:145-59.
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      99. Alber F, Förster F, Korkin D, Topf M, Sali A. Integrating diverse data for structure determination of macromolecular assemblies. Annu Rev Biochem. 2008; 77:443-77.
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      100. Robinson CV, Sali A, Baumeister W. The molecular sociology of the cell. Nature. 2007 Dec 13; 450(7172):973-82.
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      101. Almo SC, Bonanno JB, Sauder JM, Emtage S, Dilorenzo TP, Malashkevich V, Wasserman SR, Swaminathan S, Eswaramoorthy S, Agarwal R, Kumaran D, Madegowda M, Ragumani S, Patskovsky Y, Alvarado J, Ramagopal UA, Faber-Barata J, Chance MR, Sali A, Fiser A, Zhang ZY, Lawrence DS, Burley SK. Structural genomics of protein phosphatases. J Struct Funct Genomics. 2007 Sep; 8(2-3):121-40.
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      102. Bajaj K, Madhusudhan MS, Adkar BV, Chakrabarti P, Ramakrishnan C, Sali A, Varadarajan R. Stereochemical criteria for prediction of the effects of proline mutations on protein stability. PLoS Comput Biol. 2007 Dec; 3(12):e241.
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      103. Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Sali A, Rout MP. The molecular architecture of the nuclear pore complex. Nature. 2007 Nov 29; 450(7170):695-701.
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      104. Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, Devos D, Suprapto A, Karni-Schmidt O, Williams R, Chait BT, Rout MP, Sali A. Determining the architectures of macromolecular assemblies. Nature. 2007 Nov 29; 450(7170):683-94.
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      105. Sali A, Lima CD, Kostic M. Structural genomics. Structure. 2007 Nov; 15(11):1341.
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      106. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci. 2007 Nov; Chapter 2:Unit 2.9.
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      107. Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A. Host pathogen protein interactions predicted by comparative modeling. Protein Sci. 2007 Dec; 16(12):2585-96.
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      108. Cong Y, Topf M, Sali A, Matsudaira P, Dougherty M, Chiu W, Schmid MF. Crystallographic conformers of actin in a biologically active bundle of filaments. J Mol Biol. 2008 Jan 11; 375(2):331-6.
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      109. Melo F, Sali A. Fold assessment for comparative protein structure modeling. Protein Sci. 2007 Nov; 16(11):2412-26.
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      110. Feyfant E, Sali A, Fiser A. Modeling mutations in protein structures. Protein Sci. 2007 Sep; 16(9):2030-41.
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      111. Aragues R, Sali A, Bonet J, Marti-Renom MA, Oliva B. Characterization of protein hubs by inferring interacting motifs from protein interactions. PLoS Comput Biol. 2007 Sep; 3(9):1761-71.
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      112. Marti-Renom MA, Rossi A, Al-Shahrour F, Davis FP, Pieper U, Dopazo J, Sali A. The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. BMC Bioinformatics. 2007; 8 Suppl 4:S4.
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      113. Marti-Renom MA, Pieper U, Madhusudhan MS, Rossi A, Eswar N, Davis FP, Al-Shahrour F, Dopazo J, Sali A. DBAli tools: mining the protein structure space. Nucleic Acids Res. 2007 Jul; 35(Web Server issue):W393-7.
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      114. Wang SX, Pandey KC, Scharfstein J, Whisstock J, Huang RK, Jacobelli J, Fletterick RJ, Rosenthal PJ, Abrahamson M, Brinen LS, Rossi A, Sali A, McKerrow JH. The structure of chagasin in complex with a cysteine protease clarifies the binding mode and evolution of an inhibitor family. Structure. 2007 May; 15(5):535-43.
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      115. Soranzo N, Kelly L, Martinian L, Burley MW, Thom M, Sali A, Kroetz DL, Goldstein DB, Sisodiya SM. Lack of support for a role for RLIP76 (RALBP1) in response to treatment or predisposition to epilepsy. Epilepsia. 2007 Apr; 48(4):674-83.
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      116. Carvalho MA, Marsillac SM, Karchin R, Manoukian S, Grist S, Swaby RF, Urmenyi TP, Rondinelli E, Silva R, Gayol L, Baumbach L, Sutphen R, Pickard-Brzosowicz JL, Nathanson KL, Sali A, Goldgar D, Couch FJ, Radice P, Monteiro AN. Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis. Cancer Res. 2007 Feb 15; 67(4):1494-501.
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      117. Kelly L, Karchin R, Sali A. Protein interactions and disease phenotypes in the ABC transporter superfamily. Pac Symp Biocomput. 2007; 51-63.
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      118. Karchin R, Monteiro AN, Tavtigian SV, Carvalho MA, Sali A. Functional impact of missense variants in BRCA1 predicted by supervised learning. PLoS Comput Biol. 2007 Feb 16; 3(2):e26.
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      119. Winn VD, Haimov-Kochman R, Paquet AC, Yang YJ, Madhusudhan MS, Gormley M, Feng KT, Bernlohr DA, McDonagh S, Pereira L, Sali A, Fisher SJ. Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term. Endocrinology. 2007 Mar; 148(3):1059-79.
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      120. Shen MY, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci. 2006 Nov; 15(11):2507-24.
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      121. Korkin D, Davis FP, Alber F, Luong T, Shen MY, Lucic V, Kennedy MB, Sali A. Structural modeling of protein interactions by analogy: application to PSD-95. PLoS Comput Biol. 2006 Nov 10; 2(11):e153.
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      122. Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A. Comparative protein structure modeling using Modeller. Curr Protoc Bioinformatics. 2006 Oct; Chapter 5:Unit 5.6.
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      123. Rossi A, Marti-Renom MA, Sali A. Localization of binding sites in protein structures by optimization of a composite scoring function. Protein Sci. 2006 Oct; 15(10):2366-80.
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      124. Colubri A, Jha AK, Shen MY, Sali A, Berry RS, Sosnick TR, Freed KF. Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. J Mol Biol. 2006 Nov 3; 363(4):835-57.
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      125. Berman HM, Burley SK, Chiu W, Sali A, Adzhubei A, Bourne PE, Bryant SH, Dunbrack RL, Fidelis K, Frank J, Godzik A, Henrick K, Joachimiak A, Heymann B, Jones D, Markley JL, Moult J, Montelione GT, Orengo C, Rossmann MG, Rost B, Saibil H, Schwede T, Standley DM, Westbrook JD. Outcome of a workshop on archiving structural models of biological macromolecules. Structure. 2006 Aug; 14(8):1211-7.
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      126. Eramian D, Shen MY, Devos D, Melo F, Sali A, Marti-Renom MA. A composite score for predicting errors in protein structure models. Protein Sci. 2006 Jul; 15(7):1653-66.
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      127. Davis FP, Braberg H, Shen MY, Pieper U, Sali A, Madhusudhan MS. Protein complex compositions predicted by structural similarity. Nucleic Acids Res. 2006; 34(10):2943-52.
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      128. Dokudovskaya S, Williams R, Devos D, Sali A, Chait BT, Rout MP. Protease accessibility laddering: a proteomic tool for probing protein structure. Structure. 2006 Apr; 14(4):653-60.
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      129. Nguyen TD, Gow JM, Chinn LW, Kelly L, Jeong H, Huang CC, Stryke D, Kawamoto M, Johns SJ, Carlson E, Taylor T, Ferrin TE, Sali A, Giacomini KM, Kroetz DL. PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network. Pharmacol Rev. 2006 Mar; 58(1):1-2.
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      130. Devos D, Dokudovskaya S, Williams R, Alber F, Eswar N, Chait BT, Rout MP, Sali A. Simple fold composition and modular architecture of the nuclear pore complex. Proc Natl Acad Sci U S A. 2006 Feb 14; 103(7):2172-7.
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      131. Topf M, Baker ML, Marti-Renom MA, Chiu W, Sali A. Refinement of protein structures by iterative comparative modeling and CryoEM density fitting. J Mol Biol. 2006 Apr 14; 357(5):1655-68.
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      132. Madhusudhan MS, Marti-Renom MA, Sanchez R, Sali A. Variable gap penalty for protein sequence-structure alignment. Protein Eng Des Sel. 2006 Mar; 19(3):129-33.
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      133. Pieper U, Eswar N, Davis FP, Braberg H, Madhusudhan MS, Rossi A, Marti-Renom M, Karchin R, Webb BM, Eramian D, Shen MY, Kelly L, Melo F, Sali A. MODBASE: a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2006 Jan 1; 34(Database issue):D291-5.
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      134. Topf M, Sali A. Combining electron microscopy and comparative protein structure modeling. Curr Opin Struct Biol. 2005 Oct; 15(5):578-85.
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      135. McMahon SA, Miller JL, Lawton JA, Kerkow DE, Hodes A, Marti-Renom MA, Doulatov S, Narayanan E, Sali A, Miller JF, Ghosh P. The C-type lectin fold as an evolutionary solution for massive sequence variation. Nat Struct Mol Biol. 2005 Oct; 12(10):886-92.
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      136. Korkin D, Davis FP, Sali A. Localization of protein-binding sites within families of proteins. Protein Sci. 2005 Sep; 14(9):2350-60.
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      137. Dvorák J, Delcroix M, Rossi A, Vopálenský V, Pospísek M, Sedinová M, Mikes L, Sajid M, Sali A, McKerrow JH, Horák P, Caffrey CR. Multiple cathepsin B isoforms in schistosomula of Trichobilharzia regenti: identification, characterisation and putative role in migration and nutrition. Int J Parasitol. 2005 Jul; 35(8):895-910.
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      138. Espadaler J, Aragüés R, Eswar N, Marti-Renom MA, Querol E, Avilés FX, Sali A, Oliva B. Detecting remotely related proteins by their interactions and sequence similarity. Proc Natl Acad Sci U S A. 2005 May 17; 102(20):7151-6.
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      139. Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A. LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics. 2005 Jun 15; 21(12):2814-20.
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      140. Alber F, Kim MF, Sali A. Structural characterization of assemblies from overall shape and subcomplex compositions. Structure. 2005 Mar; 13(3):435-45.
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      141. Yasuda S, Morokawa N, Wong GW, Rossi A, Madhusudhan MS, Sali A, Askew YS, Adachi R, Silverman GA, Krilis SA, Stevens RL. Urokinase-type plasminogen activator is a preferred substrate of the human epithelium serine protease tryptase epsilon/PRSS22. Blood. 2005 May 15; 105(10):3893-901.
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      142. Topf M, Baker ML, John B, Chiu W, Sali A. Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. J Struct Biol. 2005 Feb; 149(2):191-203.
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      143. Davis FP, Sali A. PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics. 2005 May 1; 21(9):1901-7.
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      144. Karchin R, Kelly L, Sali A. Improving functional annotation of non-synonomous SNPs with information theory. Pac Symp Biocomput. 2005; 397-408.
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      145. Bonanno JB, Almo SC, Bresnick A, Chance MR, Fiser A, Swaminathan S, Jiang J, Studier FW, Shapiro L, Lima CD, Gaasterland TM, Sali A, Bain K, Feil I, Gao X, Lorimer D, Ramos A, Sauder JM, Wasserman SR, Emtage S, D'Amico KL, Burley SK. New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative. J Struct Funct Genomics. 2005; 6(2-3):225-32.
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      146. Maurer SM, Rai A, Sali A. Finding cures for tropical diseases: is open source an answer? PLoS Med. 2004 Dec; 1(3):e56.
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      147. Devos D, Dokudovskaya S, Alber F, Williams R, Chait BT, Sali A, Rout MP. Components of coated vesicles and nuclear pore complexes share a common molecular architecture. PLoS Biol. 2004 Dec; 2(12):e380.
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      148. Chance MR, Fiser A, Sali A, Pieper U, Eswar N, Xu G, Fajardo JE, Radhakannan T, Marinkovic N. High-throughput computational and experimental techniques in structural genomics. Genome Res. 2004 Oct; 14(10B):2145-54.
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      149. Mirkovic N, Marti-Renom MA, Weber BL, Sali A, Monteiro AN. Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition. Cancer Res. 2004 Jun 1; 64(11):3790-7.
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      150. Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. A structural perspective on protein-protein interactions. Curr Opin Struct Biol. 2004 Jun; 14(3):313-24.
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      151. Rossi A, Deveraux Q, Turk B, Sali A. Comprehensive search for cysteine cathepsins in the human genome. Biol Chem. 2004 May; 385(5):363-72.
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      152. Marti-Renom MA, Madhusudhan MS, Sali A. Alignment of protein sequences by their profiles. Protein Sci. 2004 Apr; 13(4):1071-87.
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      153. Pieper U, Eswar N, Braberg H, Madhusudhan MS, Davis FP, Stuart AC, Mirkovic N, Rossi A, Marti-Renom MA, Fiser A, Webb B, Greenblatt D, Huang CC, Ferrin TE, Sali A. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 2004 Jan 1; 32(Database issue):D217-22.
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      154. John B, Sali A. Detection of homologous proteins by an intermediate sequence search. Protein Sci. 2004 Jan; 13(1):54-62.
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      155. Fiser A, Sali A. ModLoop: automated modeling of loops in protein structures. Bioinformatics. 2003 Dec 12; 19(18):2500-1.
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      156. Sali A. NIH workshop on structural proteomics of biological complexes. Structure. 2003 Sep; 11(9):1043-7.
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      157. John B, Sali A. Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Res. 2003 Jul 15; 31(14):3982-92.
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      158. Eswar N, John B, Mirkovic N, Fiser A, Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, Madhusudhan MS, Yerkovich B, Sali A. Tools for comparative protein structure modeling and analysis. Nucleic Acids Res. 2003 Jul 1; 31(13):3375-80.
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      159. Koh IY, Eyrich VA, Marti-Renom MA, Przybylski D, Madhusudhan MS, Eswar N, Graña O, Pazos F, Valencia A, Sali A, Rost B. EVA: Evaluation of protein structure prediction servers. Nucleic Acids Res. 2003 Jul 1; 31(13):3311-5.
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      160. Gao H, Sengupta J, Valle M, Korostelev A, Eswar N, Stagg SM, Van Roey P, Agrawal RK, Harvey SC, Sali A, Chapman MS, Frank J. Study of the structural dynamics of the E coli 70S ribosome using real-space refinement. Cell. 2003 Jun 13; 113(6):789-801.
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      161. Lee SA, Shen EL, Fiser A, Sali A, Guo S. The zebrafish forkhead transcription factor Foxi1 specifies epibranchial placode-derived sensory neurons. Development. 2003 Jun; 130(12):2669-79.
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      162. Sali A, Glaeser R, Earnest T, Baumeister W. From words to literature in structural proteomics. Nature. 2003 Mar 13; 422(6928):216-25.
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      163. Ilyin VA, Pieper U, Stuart AC, Marti-Renom MA, McMahan L, Sali A. ModView, visualization of multiple protein sequences and structures. Bioinformatics. 2003 Jan; 19(1):165-6.
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      164. Fiser A, Sali A. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol. 2003; 374:461-91.
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      165. Iverson GM, Reddel S, Victoria EJ, Cockerill KA, Wang YX, Marti-Renom MA, Sali A, Marquis DM, Krilis SA, Linnik MD. Use of single point mutations in domain I of beta 2-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies. J Immunol. 2002 Dec 15; 169(12):7097-103.
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      166. Fiser A, Feig M, Brooks CL, Sali A. Evolution and physics in comparative protein structure modeling. Acc Chem Res. 2002 Jun; 35(6):413-21.
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      167. Vernal J, Fiser A, Sali A, Müller M, Cazzulo JJ, Nowicki C. Probing the specificity of a trypanosomal aromatic alpha-hydroxy acid dehydrogenase by site-directed mutagenesis. Biochem Biophys Res Commun. 2002 Apr 26; 293(1):633-9.
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      168. Yang Y, Li L, Wong GW, Krilis SA, Madhusudhan MS, Sali A, Stevens RL. 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. 2002 Jul 12; 277(28):25756-74.
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      169. Chance MR, Bresnick AR, Burley SK, Jiang JS, Lima CD, Sali A, Almo SC, Bonanno JB, Buglino JA, Boulton S, Chen H, Eswar N, He G, Huang R, Ilyin V, McMahan L, Pieper U, Ray S, Vidal M, Wang LK. Structural genomics: a pipeline for providing structures for the biologist. Protein Sci. 2002 Apr; 11(4):723-38.
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      170. Marti-Renom MA, Madhusudhan MS, Fiser A, Rost B, Sali A. Reliability of assessment of protein structure prediction methods. Structure. 2002 Mar; 10(3):435-40.
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      171. Melo F, Sánchez R, Sali A. Statistical potentials for fold assessment. Protein Sci. 2002 Feb; 11(2):430-48.
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      172. Stuart AC, Ilyin VA, Sali A. LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics. 2002 Jan; 18(1):200-1.
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      173. Pieper U, Eswar N, Stuart AC, Ilyin VA, Sali A. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res. 2002 Jan 1; 30(1):255-9.
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