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    Andrej Sali, PhD

    TitleProfessor
    SchoolUCSF School of Pharmacy
    DepartmentBioengineering
    Address1700 4th Street
    San Francisco CA 94158
    Phone415-514-4227
    vCardDownload vCard

      Collapse Biography 
      Collapse Awards and Honors
      Science Ambassador of Republic of Slovenia2007Zois Award
      2000 - 2003Irma T. Hirschl Career Award Scientist
      1998 - 2000Alfred P. Sloan Research Fellow
      1996 - 1999Alexandrine and Alexander L. Sinsheimer Scholar
      1991 - 1994Jane Coffin Childs Memorial Fund for Medical Research Postdoctoral Fellow
      1989 - 1990Merck Sharp & Dohm Academic Scholarship
      Research Council of Slovenia1987 - 1988Scholarship for Graduate Studies
      Committee of Principals and Vice Chancellors, England1987 - 1990Overseas Research Students Award
      Birkbeck College, London, UK1987British Council Visiting Student
      Birkbeck College, London, UK1985British Council Visiting Student
      J. Stefan Institute, Ljubljana, Slovenia1984 - 1987Undergraduate Scholarship

      Collapse Overview 
      Collapse Overview
      Dr. Andrej Sali is interested in using computation grounded in the laws of physics and the theory of evolution to study the structure and function of proteins. His lab aims to improve and apply methods for predicting the structures of proteins, determining the structures of macromolecular assemblies, and annotating the functions of proteins using their structures. This research contributes to structure-based functional annotation of proteins and thus enhances the impact of genome sequencing, structural genomics, and functional genomics on biology and medicine.


      Collapse ORNG Applications 
      Collapse Websites
      Collapse NIH Awarded Grants
      Collapse Global Health

      Collapse Bibliographic 
      Collapse Publications
      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.
      List All   |   Timeline
      1. Raveh B, Karp JM, Sparks S, Dutta K, Rout MP, Sali A, Cowburn D. Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex. Proc Natl Acad Sci U S A. 2016 May 3; 113(18):E2489-97. PMID: 27091992.
        View in: PubMed
      2. Sprowl JA, Ong SS, Gibson AA, Hu S, Du G, Lin W, Li L, Bharill S, Ness RA, Stecula A, Offer SM, Diasio RB, Nies AT, Schwab M, Cavaletti G, Schlatter E, Ciarimboli G, Schellens JH, Isacoff EY, Sali A, Chen T, Baker SD, Sparreboom A, Pabla N. A phosphotyrosine switch regulates organic cation transporters. Nat Commun. 2016; 7:10880. PMID: 26979622.
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      3. Greenberg CH, Kollman J, Zelter A, Johnson R, MacCoss MJ, Davis TN, Agard DA, Sali A. Structure of ?-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure. J Struct Biol. 2016 Jun; 194(3):303-10. PMID: 26968363.
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      4. Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidmann D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A, et al. CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites. J Mol Biol. 2016 Feb 4. PMID: 26854760.
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      5. LoPiccolo J, Kim SJ, Shi Y, Wu B, Wu H, Chait BT, Singer RH, Sali A, Brenowitz M, Bresnick AR, Backer JM. Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85a Homodimer. J Biol Chem. 2015 Dec 18; 290(51):30390-405. PMID: 26475863.
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      6. Rettenmaier TJ, Fan H, Karpiak J, Doak A, Sali A, Shoichet BK, Wells JA. Small-Molecule Allosteric Modulators of the Protein Kinase PDK1 from Structure-Based Docking. J Med Chem. 2015 Oct 22; 58(20):8285-91. PMID: 26443011.
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      7. Shi Y, Pellarin R, Fridy PC, Fernandez-Martinez J, Thompson MK, Li Y, Wang QJ, Sali A, Rout MP, Chait BT. A strategy for dissecting the architectures of native macromolecular assemblies. Nat Methods. 2015 Dec; 12(12):1135-8. PMID: 26436480.
        View in: PubMed
      8. Robinson PJ, Trnka MJ, Pellarin R, Greenberg CH, Bushnell DA, Davis R, Burlingame AL, Sali A, Kornberg RD. Molecular architecture of the yeast Mediator complex. Elife. 2015; 4. PMID: 26402457.
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      9. Luo J, Cimermancic P, Viswanath S, Ebmeier CC, Kim B, Dehecq M, Raman V, Greenberg CH, Pellarin R, Sali A, Taatjes DJ, Hahn S, Ranish J. Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH. Mol Cell. 2015 Sep 3; 59(5):794-806. PMID: 26340423.
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      10. Johnson JR, Santos SD, Johnson T, Pieper U, Strumillo M, Wagih O, Sali A, Krogan NJ, Beltrao P. Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes. PLoS Comput Biol. 2015 Aug; 11(8):e1004362. PMID: 26312481.
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      11. Choudhury AR, Sikorska E, van den Boom J, Bayer P, Popenda L, Szutkowski K, Jurga S, Bonomi M, Sali A, Zhukov I, Passamonti S, Novic M. Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data. PLoS One. 2015; 10(8):e0135455. PMID: 26291722.
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      12. Carter L, Kim SJ, Schneidman-Duhovny D, Stöhr J, Poncet-Montange G, Weiss TM, Tsuruta H, Prusiner SB, Sali A. Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering. Biophys J. 2015 Aug 18; 109(4):793-805. PMID: 26287631.
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      13. Smith CC, Lin K, Stecula A, Sali A, Shah NP. FLT3 D835 mutations confer differential resistance to type II FLT3 inhibitors. Leukemia. 2015 Dec; 29(12):2390-2. PMID: 26108694.
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      14. Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD. Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure. 2015 Jul 7; 23(7):1156-67. PMID: 26095030.
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      15. Lima CD, Sali A, Kostic M. Growing an editorial board for an ever expanding field. Structure. 2015 Apr 7; 23(4):605. PMID: 25862929.
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      16. Verschueren E, Von Dollen J, Cimermancic P, Gulbahce N, Sali A, Krogan NJ. Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. Curr Protoc Bioinformatics. 2015; 49:8.19.1-8.19.16. PMID: 25754993.
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      17. Kollman JM, Greenberg CH, Li S, Moritz M, Zelter A, Fong KK, Fernandez JJ, Sali A, Kilmartin J, Davis TN, Agard DA. Ring closure activates yeast ?TuRC for species-specific microtubule nucleation. Nat Struct Mol Biol. 2015 Feb; 22(2):132-7. PMID: 25599398.
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      18. Politis A, Schmidt C, Tjioe E, Sandercock AM, Lasker K, Gordiyenko Y, Russel D, Sali A, Robinson CV. Topological Models of Heteromeric Protein Assemblies from Mass Spectrometry: Application to the Yeast eIF3:eIF5 Complex. Chem Biol. 2015 Jan 22; 22(1):117-28. PMID: 25544043.
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      19. Medema MH, Cimermancic P, Sali A, Takano E, Fischbach MA. A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis. PLoS Comput Biol. 2014 Dec; 10(12):e1004016. PMID: 25474254.
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      20. Webb B, Sali A. Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics. 2014; 47:5.6.1-5.6.32. PMID: 25199792.
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      21. Schneidman-Duhovny D, Pellarin R, Sali A. Uncertainty in integrative structural modeling. Curr Opin Struct Biol. 2014 Oct; 28:96-104. PMID: 25173450.
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      22. Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CH, Cimermancic P, Boehringer D, Sali A, Aebersold R, Ban N. Molecular architecture of the 40S·eIF1·eIF3 translation initiation complex. Cell. 2014 Aug 28; 158(5):1123-35. PMID: 25171412; PMCID: PMC4151992.
      23. Shi Y, Fernandez-Martinez J, Tjioe E, Pellarin R, Kim SJ, Williams R, Schneidman-Duhovny D, Sali A, Rout MP, Chait BT. Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex. Mol Cell Proteomics. 2014 Nov; 13(11):2927-43. PMID: 25161197; PMCID: PMC4223482 [Available on 11/01/15].
      24. Bonomi M, Pellarin R, Kim SJ, Russel D, Sundin BA, Riffle M, Jaschob D, Ramsden R, Davis TN, Muller EG, Sali A. Determining Protein Complex Structures Based on a Bayesian Model of in Vivo Förster Resonance Energy Transfer (FRET) Data. Mol Cell Proteomics. 2014 Nov; 13(11):2812-23. PMID: 25139910; PMCID: PMC4223474 [Available on 11/01/15].
      25. Kim SJ, Fernandez-Martinez J, Sampathkumar P, Martel A, Matsui T, Tsuruta H, Weiss TM, Shi Y, Markina-Inarrairaegui A, Bonanno JB, Sauder JM, Burley SK, Chait BT, Almo SC, Rout MP, Sali A. Integrative structure-function mapping of the nucleoporin nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex. Mol Cell Proteomics. 2014 Nov; 13(11):2911-26. PMID: 25139911; PMCID: PMC4223481 [Available on 11/01/15].
      26. Zeng-Elmore X, Gao XZ, Pellarin R, Schneidman-Duhovny D, Zhang XJ, Kozacka KA, Tang Y, Sali A, Chalkley RJ, Cote RH, Chu F. Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling. J Mol Biol. 2014 Nov 11; 426(22):3713-28. PMID: 25149264; PMCID: PMC4253074 [Available on 11/11/15].
      27. Molnar KS, Bonomi M, Pellarin R, Clinthorne GD, Gonzalez G, Goldberg SD, Goulian M, Sali A, DeGrado WF. Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ. Structure. 2014 Sep 2; 22(9):1239-51. PMID: 25087511.
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      28. Algret R, Fernandez-Martinez J, Shi Y, Kim SJ, Pellarin R, Cimermancic P, Cochet E, Sali A, Chait BT, Rout MP, Dokudovskaya S. Molecular Architecture and Function of the SEA Complex, a Modulator of the TORC1 Pathway. Mol Cell Proteomics. 2014 Nov; 13(11):2855-70. PMID: 25073740; PMCID: PMC4223477 [Available on 11/01/15].
      29. Cimermancic P, Medema MH, Claesen J, Kurita K, Wieland Brown LC, Mavrommatis K, Pati A, Godfrey PA, Koehrsen M, Clardy J, Birren BW, Takano E, Sali A, Linington RG, Fischbach MA. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters. Cell. 2014 Jul 17; 158(2):412-21. PMID: 25036635; PMCID: PMC4123684 [Available on 07/17/15].
      30. Dong GQ, Calhoun S, Fan H, Kalyanaraman C, Branch MC, Mashiyama ST, London N, Jacobson MP, Babbitt PC, Shoichet BK, Armstrong RN, Sali A. Prediction of substrates for glutathione transferases by covalent docking. J Chem Inf Model. 2014 Jun 23; 54(6):1687-99. PMID: 24802635; PMCID: PMC4068255 [Available on 05/06/15].
      31. Street TO, Zeng X, Pellarin R, Bonomi M, Sali A, Kelly MJ, Chu F, Agard DA. Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone. J Mol Biol. 2014 Jun 12; 426(12):2393-404. PMID: 24726919.
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      32. Webb B, Sali A. Protein structure modeling with MODELLER. Methods Mol Biol. 2014; 1137:1-15. PMID: 24573470.
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      33. Webb B, Lasker K, Velázquez-Muriel J, Schneidman-Duhovny D, Pellarin R, Bonomi M, Greenberg C, Raveh B, Tjioe E, Russel D, Sali A. Modeling of proteins and their assemblies with the Integrative Modeling Platform. Methods Mol Biol. 2014; 1091:277-95. PMID: 24203340.
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      34. Spill YG, Kim SJ, Schneidman-Duhovny D, Russel D, Webb B, Sali A, Nilges M. SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes. J Synchrotron Radiat. 2014 Jan; 21(Pt 1):203-8. PMID: 24365937; PMCID: PMC3874021.
      35. Pieper U, Webb BM, Dong GQ, Schneidman-Duhovny D, Fan H, Kim SJ, Khuri N, Spill YG, Weinkam P, Hammel M, Tainer JA, Nilges M, Sali A. ModBase, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2014 Jan; 42(Database issue):D336-46. PMID: 24271400; PMCID: PMC3965011.
      36. Ryan CJ, Cimermancic P, Szpiech ZA, Sali A, Hernandez RD, Krogan NJ. High-resolution network biology: connecting sequence with function. Nat Rev Genet. 2013 Dec; 14(12):865-79. PMID: 24197012; PMCID: PMC4023809 [Available on 12/01/14].
      37. Berlin K, Castañeda CA, Schneidman-Duhovny D, Sali A, Nava-Tudela A, Fushman D. Recovering a representative conformational ensemble from underdetermined macromolecular structural data. J Am Chem Soc. 2013 Nov 6; 135(44):16595-609. PMID: 24093873; PMCID: PMC3902174.
      38. Martínez-Jiménez F, Papadatos G, Yang L, Wallace IM, Kumar V, Pieper U, Sali A, Brown JR, Overington JP, Marti-Renom MA. Target prediction for an open access set of compounds active against Mycobacterium tuberculosis. PLoS Comput Biol. 2013; 9(10):e1003253. PMID: 24098102; PMCID: PMC3789770.
      39. Dong GQ, Fan H, Schneidman-Duhovny D, Webb B, Sali A. Optimized atomic statistical potentials: assessment of protein interfaces and loops. Bioinformatics. 2013 Dec 15; 29(24):3158-66. PMID: 24078704; PMCID: PMC3842762 [Available on 12/15/14].
      40. Weinkam P, Sali A. Mapping polymerization and allostery of hemoglobin S using point mutations. J Phys Chem B. 2013 Oct 24; 117(42):13058-68. PMID: 23957820; PMCID: PMC3973026.
      41. Goble AM, Toro R, Li X, Ornelas A, Fan H, Eswaramoorthy S, Patskovsky Y, Hillerich B, Seidel R, Sali A, Shoichet BK, Almo SC, Swaminathan S, Tanner ME, Raushel FM. Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. Biochemistry. 2013 Sep 17; 52(37):6525-36. PMID: 23972005; PMCID: PMC3813303.
      42. Hitchcock DS, Fan H, Kim J, Vetting M, Hillerich B, Seidel RD, Almo SC, Shoichet BK, Sali A, Raushel FM. Structure-guided discovery of new deaminase enzymes. J Am Chem Soc. 2013 Sep 18; 135(37):13927-33. PMID: 23968233; PMCID: PMC3827683.
      43. Lima CD, Sali A, Kostic M. Celebrating 20 years of Structure. Structure. 2013 Sep 3; 21(9):1477-8. PMID: 24010704.
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      44. Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. Accurate SAXS profile computation and its assessment by contrast variation experiments. Biophys J. 2013 Aug 20; 105(4):962-74. PMID: 23972848; PMCID: PMC3752106.
      45. Pandya C, Brown S, Pieper U, Sali A, Dunaway-Mariano D, Babbitt PC, Xia Y, Allen KN. Consequences of domain insertion on sequence-structure divergence in a superfold. Proc Natl Acad Sci U S A. 2013 Sep 3; 110(36):E3381-7. PMID: 23959887; PMCID: PMC3767544.
      46. Trewhella J, Hendrickson WA, Kleywegt GJ, Sali A, Sato M, Schwede T, Svergun DI, Tainer JA, Westbrook J, Berman HM. Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB. Structure. 2013 Jun 4; 21(6):875-81. PMID: 23747111.
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      47. Waight AB, Pedersen BP, Schlessinger A, Bonomi M, Chau BH, Roe-Zurz Z, Risenmay AJ, Sali A, Stroud RM. Structural basis for alternating access of a eukaryotic calcium/proton exchanger. Nature. 2013 Jul 4; 499(7456):107-10. PMID: 23685453; PMCID: PMC3702627.
      48. 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. PMID: 23569277; PMCID: PMC3637775.
      49. 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. PMID: 23542591; PMCID: PMC3678552.
      50. 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. PMID: 23509259; PMCID: PMC3619328.
      51. 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. PMID: 23499021; PMCID: PMC3755625.
      52. 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. PMID: 23473666; PMCID: PMC3840220.
      53. Ward AB, Sali A, Wilson IA. Biochemistry. Integrative structural biology. Science. 2013 Feb 22; 339(6122):913-5. PMID: 23430643; PMCID: PMC3633482.
      54. 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. PMID: 23381628; PMCID: PMC3645303.
      55. 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. PMID: 23241029; PMCID: PMC4068829.
      56. 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. PMID: 23256477; PMCID: PMC3557803.
      57. Schlessinger A, Khuri N, Giacomini KM, Sali A. Molecular modeling and ligand docking for solute carrier (SLC) transporters. Curr Top Med Chem. 2013; 13(7):843-56. PMID: 23578028; PMCID: PMC4056341.
      58. 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. PMID: 23228330; PMCID: PMC3557769.
      59. 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. PMID: 23185482; PMCID: PMC3503826.
      60. 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. PMID: 23112201; PMCID: PMC3503186.
      61. 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 15; 28(24):3282-9. PMID: 23093611; PMCID: PMC3519461.
      62. 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. PMID: 22974364; PMCID: PMC3496023.
      63. 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. PMID: 22899687; PMCID: PMC3420364.
      64. 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. PMID: 22955930.
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      65. 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. PMID: 22932902; PMCID: PMC3488050.
      66. Schneidman-Duhovny D, Kim SJ, Sali A. Integrative structural modeling with small angle X-ray scattering profiles. BMC Struct Biol. 2012; 12:17. PMID: 22800408; PMCID: PMC3427135.
      67. 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. PMID: 22544723; PMCID: PMC3686472.
      68. 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. PMID: 22645316; PMCID: PMC3412957.
      69. 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. PMID: 22618536; PMCID: PMC3400954.
      70. 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. PMID: 22609626; PMCID: PMC3723349.
      71. 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. PMID: 22403063; PMCID: PMC3324024.
      72. 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. PMID: 22718633; PMCID: PMC4111641.
      73. 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. PMID: 22331846; PMCID: PMC3283990.
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      83. 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. PMID: 21999478; PMCID: PMC3238057.
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      87. 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. PMID: 21885739; PMCID: PMC3179104.
      88. Goble AM, Fan H, Sali A, Raushel FM. Discovery of a cytokinin deaminase. ACS Chem Biol. 2011 Oct 21; 6(10):1036-40. PMID: 21823622; PMCID: PMC3199332.
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      99. 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. PMID: 20859243; PMCID: PMC2976715.
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      105. 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. PMID: 20505003; PMCID: PMC2894511.
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      107. 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. PMID: 20457942; PMCID: PMC2906887.
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      152. 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. PMID: 18046405.
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      153. Sali A, Lima CD, Kostic M. Structural genomics. Structure. 2007 Nov; 15(11):1341. PMID: 17997955.
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      154. 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. PMID: 18429317.
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      155. 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. PMID: 17965183; PMCID: PMC2222825.
      156. 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. PMID: 18022194; PMCID: PMC2680129.
      157. Melo F, Sali A. Fold assessment for comparative protein structure modeling. Protein Sci. 2007 Nov; 16(11):2412-26. PMID: 17905832; PMCID: PMC2211691.
      158. Feyfant E, Sali A, Fiser A. Modeling mutations in protein structures. Protein Sci. 2007 Sep; 16(9):2030-41. PMID: 17766392; PMCID: PMC2206969.
      159. 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. PMID: 17941705; PMCID: PMC1976338.
      160. 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. PMID: 17570147; PMCID: PMC1892083.
      161. 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. PMID: 17478513; PMCID: PMC1933139.
      162. 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. PMID: 17502099.
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      163. 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. PMID: 17437410.
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      164. 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. PMID: 17308087; PMCID: PMC2936786.
      165. Kelly L, Karchin R, Sali A. Protein interactions and disease phenotypes in the ABC transporter superfamily. Pac Symp Biocomput. 2007; 51-63. PMID: 17990484.
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      166. 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. PMID: 17305420; PMCID: PMC1797820.
      167. 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. PMID: 17170095.
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      168. Shen MY, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci. 2006 Nov; 15(11):2507-24. PMID: 17075131; PMCID: PMC2242414.
      169. 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. PMID: 17096593; PMCID: PMC1635541.
      170. 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. PMID: 18428767; PMCID: PMC4186674.
      171. 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. PMID: 16963645; PMCID: PMC2242385.
      172. 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. PMID: 16982067.
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      173. 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. PMID: 16955948.
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      174. 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. PMID: 16751606; PMCID: PMC2242555.
      175. 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. PMID: 16738133; PMCID: PMC1474056.
      176. 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. PMID: 16615907.
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      177. 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. PMID: 16507877.
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      178. 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. PMID: 16461911; PMCID: PMC1413685.
      179. 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. PMID: 16490207.
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      180. 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. PMID: 16423846.
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      181. 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. PMID: 16381869; PMCID: PMC1347422.
      182. Topf M, Sali A. Combining electron microscopy and comparative protein structure modeling. Curr Opin Struct Biol. 2005 Oct; 15(5):578-85. PMID: 16118050.
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      183. 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. PMID: 16170324.
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      184. Korkin D, Davis FP, Sali A. Localization of protein-binding sites within families of proteins. Protein Sci. 2005 Sep; 14(9):2350-60. PMID: 16081657; PMCID: PMC2253467.
      185. 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. PMID: 15950230.
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      186. 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. PMID: 15883372; PMCID: PMC1129109.
      187. 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. PMID: 15827081.
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      188. Alber F, Kim MF, Sali A. Structural characterization of assemblies from overall shape and subcomplex compositions. Structure. 2005 Mar; 13(3):435-45. PMID: 15766545.
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      189. 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. PMID: 15701722; PMCID: PMC1895090.
      190. 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. PMID: 15681235.
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      191. Davis FP, Sali A. PIBASE: a comprehensive database of structurally defined protein interfaces. Bioinformatics. 2005 May 1; 21(9):1901-7. PMID: 15657096.
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      192. Karchin R, Kelly L, Sali A. Improving functional annotation of non-synonomous SNPs with information theory. Pac Symp Biocomput. 2005; 397-408. PMID: 15759645.
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      193. 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. PMID: 16211523.
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      194. Maurer SM, Rai A, Sali A. Finding cures for tropical diseases: is open source an answer? PLoS Med. 2004 Dec; 1(3):e56. PMID: 15630466; PMCID: PMC539047.
      195. 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. PMID: 15523559; PMCID: PMC524472.
      196. 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. PMID: 15489337; PMCID: PMC528931.
      197. 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. PMID: 15172985.
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      198. 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. PMID: 15193311.
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      199. 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. PMID: 15195995.
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      200. Marti-Renom MA, Madhusudhan MS, Sali A. Alignment of protein sequences by their profiles. Protein Sci. 2004 Apr; 13(4):1071-87. PMID: 15044736; PMCID: PMC2280052.
      201. 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. PMID: 14681398; PMCID: PMC308829.
      202. John B, Sali A. Detection of homologous proteins by an intermediate sequence search. Protein Sci. 2004 Jan; 13(1):54-62. PMID: 14691221; PMCID: PMC2286512.
      203. Fiser A, Sali A. ModLoop: automated modeling of loops in protein structures. Bioinformatics. 2003 Dec 12; 19(18):2500-1. PMID: 14668246.
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      204. Sali A. NIH workshop on structural proteomics of biological complexes. Structure. 2003 Sep; 11(9):1043-7. PMID: 12962622.
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      205. 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. PMID: 12853614; PMCID: PMC165975.
      206. 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. PMID: 12824331; PMCID: PMC168950.
      207. 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. PMID: 12824315; PMCID: PMC169025.
      208. 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. PMID: 12809609.
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      209. 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. PMID: 12736211.
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      210. Sali A, Glaeser R, Earnest T, Baumeister W. From words to literature in structural proteomics. Nature. 2003 Mar 13; 422(6928):216-25. PMID: 12634795.
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      211. 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. PMID: 12499313.
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      212. Fiser A, Sali A. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol. 2003; 374:461-91. PMID: 14696385.
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      213. 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. PMID: 12471146.
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      214. 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. PMID: 12069626.
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      215. 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. PMID: 12054650.
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      216. 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. PMID: 11956218.
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      217. 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. PMID: 11910018; PMCID: PMC2373525.
      218. 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. PMID: 12005441.
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      219. Melo F, Sánchez R, Sali A. Statistical potentials for fold assessment. Protein Sci. 2002 Feb; 11(2):430-48. PMID: 11790853; PMCID: PMC2373452.
      220. 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. PMID: 11836232.
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      221. 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. PMID: 11752309; PMCID: PMC99112.
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