Publications
1. M. Renko, A. Sali, V. Turk, M. Pokomy, I. Kregar. "A neutral metalloproteinase from Streptomyces rimosus." Vestnik Slovenskega Kemijskega Drustva 32/2, 161-173, 1985.

2. B. Lenarcic, A. Ritonja, A. Sali, M. Kotnik, V. Turk, W. Machleidt. "Properties and structure of human spleen stefin B - a low molecular weight protein inhibitor of cysteine proteinases." In: Cysteine Proteinases and Their Inhibitors; First International Symposium, Portoroz, Yugoslavia, September 15-18, 1985. Xvi+846p. Ed: V. Turk, pp. 473-488, Walter De Gruyter and Co., Berlin, West Germany; New York, New York, USA., 1986.

3. V. Turk, J. Brzin, B. Lenarcic, A. Sali, W. Machleidt. "Human stefins and cystatis: their properties and structural relationships." In: Cysteine Proteinases and Their Inhibitors; First International Symposium, Portoroz, Yugoslavia, September 15-18, 1985. Xvi+846p. Ed: V. Turk, pp. 429-442, Walter De Gruyter and Co., Berlin, West Germany; New York, New York, USA., 1986.

4. M. Kotnik, A. Sali, J. Kos, B. Turk, V. Turk. "Nova metoda za hitro dolocanje kineticnih konstant pri interakciji encima s kompetitivnim inhibitorjem (A new method for rapid determination of kinetic constants for competitive inhibition of enzymes)." Vestnik Slovenskaga Kemijskega Drustva 34, 369-377, 1987.

5. A. Sali, V. Turk. "Prediction of the secondary structures of stefins and cystatins, the low-molecular mass protein inhibitors of cysteine proteinases." Biol Chem Hoppe Seyler 368, 493-499, 1987.

6. T. Lah, I. Kregar, A. Sali, B. Lenarcic, M. Kotnik, V. Kostka, V. Turk. "Circular dichroism studies of different aspartyl proteinases and their interactions with pepstatin." Periodicum Biologorum 90, 31-38, 1988.

7. V. Turk, R. Jerala, B. Lenarcic, A. Sali. "Structural and functional aspects of human cathepsins B." In: Intracellular Proteolysis: Mechanisms and Regulations. Ed: N. Katunuma, E. Kominami, pp. 27 -37, Japan Scientific Societies Press, 1989.

8. A. Sali, B. Veerapandian, J.B. Cooper, S.I. Foundling, D.J. Hoover, T.L. Blundell. "High-resolution X-ray diffraction study of the complex between endothiapepsin and an oligopeptide inhibitor: the analysis of the inhibitor binding and description of the rigid body shift in the enzyme." Embo Journal 8, 2179-2188, 1989.

9. T.L. Blundell, G. Elliott, S.P. Gardner, T. Hubbard, S. Islam, M. Johnson, D. Mantafounis, P. Murrayrust, J. Overington, J.E. Pitts, A. Sali, B.L. Sibanda, J. Singh, M.J.E. Sternberg, M.J. Sutcliffe, J.M. Thornton, P. Travers. "Protein engineering and design." Philosophical Transactions of the Royal Society of London Series B-Biological Sciences 324, 447-460, 1989.

10. T.L. Blundell, D. Carney, T. Hubbard, M.S. Johnson, A. McLeod, J.P. Overington, A. Sali, M.S. Sutcliffe, P. Thomas. "Knowledge-based protein modelling and design." In: Advances in Protein Design: International Workshop 1988 GBF Monographs. Ed: H. Bloecker, J. Collins, R.D. Schmid, D. Schomburg, 12, pp. 39-43, VCH, 1989.

11. A. Sali, T.L. Blundell. "Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming." J Mol Biol 212, 403-428, 1990.

12. A. Sali, J.P. Overington, M.S. Johnson, T.L. Blundell. "From Comparisons of protein sequences and structures to protein modelling and design." Trends Biochem Sci 15, 235-240, 1990.

13. B. Veerapandian, J.B. Cooper, A. Sali, T.L. Blundell. "X-ray analyses of aspartic proteinases. III Three-dimensional structure of endothiapepsin complexed with a transition-state isostere inhibitor of renin at 1.6 A resolution." J Mol Biol 216, 1017-1029, 1990.

14. J. Overington, M.S. Johnson, A. Sali, T.L. Blundell. "Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction." Procedures in Biological Science 241, 132-145, 1990.

15. J.P. Overington, M.S. Johnson, C. Topham, A. McLeod, A. Sali, Z.Y. Zhu, L. Sibanda, T.L. Blundell. "Applications of environment specific amino acid substitution tables to identification of key residues in protein tertiary structure." Curr Sci 59, 867-874, 1990.

16. M.S. Johnson, A. Sali, T.L. Blundell. "Phylogenetic relationships from three-dimensional protein structures." Methods Enzymol 183, 670-690, 1990.

17. M.S. Johnson, J.P. Overington, A. Sali. "Knowledge-based protein modelling: Human plasma kallikrein and human neutrophil defensin." In: Chemistry: Techniques Structure and Function. Ed: J.J. Vilafranca, pp. 567-574, Academic Press, Inc., 1990.

18. M.S. Johnson, J. Overington, A. Sali, Z. Zhu, D. Donnelly, P. Thomas, A. McLeod, R. Goold, C. Topham, T.L. Blundell. "From comparative structure analysis to protein engineering: Knowledge-based protein modelling and design." Fresenius Journal of Analytic Chemistry 337, 1-3, 1990.

19. T.L. Blundell, M.S. Johnson, J.P. Overington, A. Sali. "Knowledge-based protein modeling and the design of novel molecules." In: Protein design and the development of new therapeutics and vaccines. Ed: J.B. Hook, G. Poste, pp. 209-227, Plenum Press, New York, NY, 1990.

20. T.L. Blundell, J.B. Cooper, A. Sali, Z.Y. Zhu. "Comparisons of the sequences, 3-D structures and mechanisms of pepsin-like and retroviral aspartic proteinases." Adv Exp Med Biol 306, 443-453, 1991.

21. T.L. Blundell, J.B. Cooper, D. Donnelly, H. Driessen, Y. Edwards, F. Eisenmenger, C. Frazao, M. Johnson, K. Niefind, M. Newman, J. Overington, A. Sali, C. Slingsby, V. Nalini, Z.Y. Zhu. "Patterns of sequence variation in families of homologous proteins." In: Methods in Protein Sequence Analysis. Ed: H. Jornval, J.O. Hoog, A.M. Gustavsson, pp. 373-385, Birkhauser Verlag, Basel, Switzerland, 1991.

22. A. Sali, J.P. Overington, M.S. Johnson, T.L. Blundell. "From modelling homologous proteins to prediction of structure." In: Protein design and the development of new therapeutics and vaccines. Ed: J.M. Goodfellow, D.S. Moss, pp. 231-245, Ellis Horwood Ltd., 1991.

23. A. Sali, B. Veerapandian, J.B. Cooper, D.S. Moss, T. Hofmann, T.L. Blundell. "Domain flexibility in aspartic proteinases." Proteins 12, 158-170, 1992.

24. B. Veerapandian, J.B. Cooper, A. Sali, T.L. Blundell, R.L. Rosati, B.W. Dominy, D.B. Damon, D.J. Hoover. "Direct observation by X-ray analysis of the tetrahedral "intermediate" of aspartic proteinases." Protein Sci 1, 322-328, 1992.

25. Z.Y. Zhu, A. Sali, T.L. Blundell. "A variable gap penalty function and feature weights for protein 3-D structure comparisons." Protein Eng 5, 43-51, 1992.

26. J. Overington, D. Donnelly, M.S. Johnson, A. Sali, T.L. Blundell. "Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds." Protein Sci 1, 216-226, 1992.

27. M.S. Johnson, J.P. Overington, A. Sali, T.L. Blundell. "From the comparative analysis of proteins to similarity-based modelling." In: Computer Modelling of Biomolecular Processes. Ed: V.A. Ratner, N.A. Kolchanov, pp. 191-196, Nova Science Publishers, 1992.

28. J.P. Overington, Z.Y. Zhu, A. Sali, M.S. Johnson, R. Sowdhamini, G.V. Louie, T.L. Blundell. "Molecular recognition in protein families: a database of aligned three-dimensional structures of related proteins." Biochem Soc Trans 21 ( Pt 3), 597-604, 1993.

29. A. Sali, T.L. Blundell. "Comparative protein modelling by satisfaction of spatial restraints." J Mol Biol 234, 779-815, 1993.

30. A. Sali, R. Matsumoto, H.P. McNeil, M. Karplus, R.L. Stevens. "Three-dimensional models of four mouse mast cell chymases. Identification of proteoglycan-binding regions and protease-specific antigenic epitopes." J Biol Chem 268, 9023-9034, 1993.

31. A. Sali, T. Blundell. "Comparative protein modeling by statisfaction of spatial restraints." In: Protein Structure by Distance Analysis. Ed: H. Bohr, S. Brunak, pp. 64-86, TECH UNIV DENMARK, CTR BIOL SEQUENCE ANAL, LYNGBY, DENMARK, 1994.

32. A. Sali, J.P. Overington. "Derivation of rules for comparative protein modeling from a database of protein structure alignments." Protein Sci 3, 1582-1596, 1994.

33. A. Sali, E. Shakhnovich, M. Karplus. "Kinetics of protein folding. A lattice model study of the requirements for folding to the native state." J Mol Biol 235, 1614-1636, 1994.

34. A. Sali, E. Shakhnovich, M. Karplus. "How does a protein fold?" Nature 369, 248-251, 1994.

35. A. Dinner, A. Sali, M. Karplus, E. Shakhnovich. "Phase diagram of a model protein derived by exhaustive enumeration of the conformations." J Chem Phys 101, 1444-1451, 1994.

36. M. Karplus, A. Sali. "Theoretical studies of protein folding and unfolding." Curr Opin Struct Biol 5, 58-73, 1995.

37. M. Karplus, A. Caflisch, A. Sali, E. Shakhnovich. "Protein dynamics: From the native to the unfolded state and back again." In: Modelling of Biomolecular Structures and Mechanisms. Ed: A.Pullmanet al, pp. 69-84, Kluwer Academic Publishers, 1995.

38. A. Sali. "MODELLER: Implementing 3D protein modeling." In: mc^2, 2, pp. 5, Molecular Simulations Inc., 1995.

39. X.D. Wu, B. Knudsen, S.M. Feller, J. Zheng, A. Sali, D. Cowburn, H. Hanafusa, J. Kuriyan. "Structural basis for the specific interaction of lysine-containing proline-rich peptides with the amino-terminal SH3 domain of c-Crk." Structure 3, 215-226, 1995.

40. R. Matsumoto, A. Sali, N. Ghildyal, M. Karplus, R.L. Stevens. "Packaging of proteases and proteoglycans in the granules of mast cells and other hematopoietic cells. A cluster of histidines on mouse mast cell protease 7 regulates its binding to heparin serglycin proteoglycans." J Biol Chem 270, 19524-19531, 1995.

41. A. Sali. "Comparative protein modeling by satisfaction of spatial restraints." Mol Med Today 1, 270-277, 1995.

42. A. Sali, E. Shakhnovich, M. Karplus. "Protein Folding Studied by Monte Carlo Simulations." In: Protein Folds: A Distance Based Approach. Ed: H. Bohr, S. Brunak, pp. 202-216, CRC Press Inc., 1995.

43. A. Sali, E. Shakhnovich, M. Karplus. "Thermodynamics and kinetics of protein folding from lattice Monte Carlo simulations." In: DIMACS Series in Discrete Mathematics and Theoretical Computer Science. Ed: D. Shalloway, G. Xue, P. Pardalos, 23, pp. 199-213, American Mathematical Society, 1995.

44. A. Sali, L. Potterton, F. Yuan, H. van Vlijmen, M. Karplus. "Evaluation of comparative protein modeling by MODELLER." Proteins 23, 318-326, 1995.

45. A. Sali. "Modeling mutations and homologous proteins." Curr Opin Biotechnol 6, 437-451, 1995.

46. M. Karplus, A. Sali, E. Shakhnovich. "Kinetics of protein folding." Nature 373, 664-665, 1995.

47. Y. Sheng, A. Sali, H. Herzog, J. Lahnstein, S.A. Krilis. "Site-directed mutagenesis of recombinant human beta 2-glycoprotein I identifies a cluster of lysine residues that are critical for phospholipid binding and anti-cardiolipin antibody activity." J Immunol 157, 3744-3751, 1996.

48. N. Ghildyal, D.S. Friend, R.L. Stevens, K.F. Austen, C. Huang, J.F. Penrose, A. Sali, M.F. Gurish. "Fate of two mast cell tryptases in V3 mastocytosis and normal BALB/c mice undergoing passive systemic anaphylaxis: prolonged retention of exocytosed mMCP-6 in connective tissues, and rapid accumulation of enzymatically active mMCP-7 in the blood." The Journal of Experimental Medicine 184, 1061-1073, 1996.

49. L.Z. Xu, R. Sanchez, A. Sali, N. Heintz. "Ligand specificity of brain lipid-binding protein." J Biol Chem 271, 24711-24719, 1996.

50. A.R. Dinner, A. Sali, M. Karplus. "The folding mechanism of larger model proteins: role of native structure." Proc Natl Acad Sci U S A 93, 8356-8361, 1996.

51. S. Wu, H. de Lencastre, A. Sali, A. Tomasz. "A phosphoglucomutase-like gene essential for the optimal expression of methicillin resistance in Staphylococcus aureus: molecular cloning and DNA sequencing." Microbial Drug Resistance 2, 277-286, 1996.

52. M. Russel, N.A. Linderoth, A. Sali. "Filamentous phage assembly: variation on a protein export theme." Gene 192, 23-32, 1997.

53. C. Huang, G.W. Wong, N. Ghildyal, M.F. Gurish, A. Sali, R. Matsumoto, W.T. Qiu, R.L. Stevens. "The tryptase, mouse mast cell protease 7, exhibits anticoagulant activity in vivo and in vitro due to its ability to degrade fibrinogen in the presence of the diverse array of protease inhibitors in plasma." J Biol Chem 272, 31885-31893, 1997.

54. R. Sanchez, A. Sali. "Comparative protein modeling as an optimization problem." Journal of Molecular Structure (Theochem) 398, 489-496, 1997.

55. R. Sanchez, A. Sali. "Advances in comparative protein-structure modelling." Curr Opin Struct Biol 7, 206-214, 1997.

56. D. Koulich, M. Orlova, A. Malhotra, A. Sali, S.A. Darst, S. Borukhov. "Domain organization of Escherichia coli transcript cleavage factors GreA and GreB." J Biol Chem 272, 7201-7210, 1997.

57. J.E. Hunt, D.S. Friend, M.F. Gurish, E. Feyfant, A. Sali, C. Huang, N. Ghildyal, S. Stechschulte, K.F. Austen, R.L. Stevens. "Mouse mast cell protease 9, a novel member of the chromosome 14 family of serine proteases that is selectively expressed in uterine mast cells." J Biol Chem 272, 29158-29166, 1997.

58. R. Sanchez, A. Sali. "Evaluation of comparative protein structure modeling by MODELLER-3." Proteins Suppl 1, 50-58, 1997.

59. B. Guenther, R. Onrust, A. Sali, M. O'Donnell, J. Kuriyan. "Crystal structure of the delta' subunit of the clamp-loader complex of E. coli DNA polymerase III." Cell 91, 335-345, 1997.

60. R. Sanchez, A.Ya. Badretdinov, E. Feyfant, A. Sali. "Homology protein structure modeling." Transactions of the American Crystallographic Association 32, 81-91, 1997.

61. Y. Sheng, S.A. Krilis, A. Sali. "Site-directed mutagenesis of recombinant human beta 2-glycoprotein I. Effect of phospholipid binding and anticardiolipin antibody activity." Ann N Y Acad Sci 815, 331-333, 1997.

62. C.M. Dobson, A. Sali, M. Karplus. "Protein folding: A perspective from theory and experiment." Angewandte Chemie Int Ed 37, 868-893, 1998.

63. C. Huang, A. Sali, R.L. Stevens. "Regulation and function of mast cell proteases in inflammation." J Clin Immunol 18, 169-183, 1998.

64. D.A. Kandiah, A. Sali, Y. Sheng, E.J. Victoria, D.M. Marquis, S.M. Coutts, S.A. Krilis. "Current insights into the "antiphospholipid" syndrome: clinical, immunological, and molecular aspects." Advanced Immunology Journal 70, 507-563, 1998.

65. A. Gutin, A. Sali, V. Abkevich, M. Karplus, E. Shakhnovich. "Temperature dependence of the folding rate in a simple protein model: Search for a glass transition." J Chem Phys 108, 6466-6483, 1998.

66. E. Wolf, A. Vassilev, Y. Makino, A. Sali, Y. Nakatani, S.K. Burley. "Crystal structure of a GCN5-related N-acetyltransferase: Serratia marcescens aminoglycoside 3-N-acetyltransferase." Cell 94, 439-449, 1998.

67. R. Sanchez, A. Sali. "Large-scale protein structure modeling of the Saccharomyces cerevisiae genome." Proc Natl Acad Sci U S A 95, 13597-13602, 1998.

68. A. Sali. "100,000 protein structures for the biologist." Nat Struct Biol 5, 1029-1032, 1998.

69. R. Sanchez, A. Sali. "MODBASE: A database of comparative protein structure models." Bioinformatics 15, 1060-1061, 1999.

70. R. Sanchez, A. Sali. "Comparative protein structure modeling in genomics." Journal of Computational Physics 151, 388-401, 1999.

71. G. Wu, A. Fiser, B. ter Kuile, A. Sali, M. Muller. "Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase." Proc Natl Acad Sci U S A 96, 6285-6290, 1999.

72. T. Nagata, V. Gupta, D. Sorce, W.Y. Kim, A. Sali, B.T. Chait, K. Shigesada, Y. Ito, M.H. Werner. "Immunoglobulin motif DNA recognition and heterodimerization of the PEBP2/CBF Runt domain." Nat Struct Biol 6, 615-619, 1999.

73. J.M. Miwa, I. Ibanez-Tallon, G.W. Crabtree, R. Sanchez, A. Sali, L.W. Role, N. Heintz. "lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine receptors in the mammalian CNS." Neuron 23, 105-114, 1999.

74. G.W. Wong, Y. Tang, E. Feyfant, A. Sali, L. Li, Y. Li, C. Huang, D.S. Friend, S.A. Krilis, R.L. Stevens. "Identification of a new member of the tryptase family of mouse and human mast cell proteases which possesses a novel COOH-terminal hydrophobic extension." J Biol Chem 274, 30784-30793, 1999.

75. S.K. Burley, S.C. Almo, J.B. Bonanno, M. Capel, M.R. Chance, T. Gaasterland, D. Lin, A. Sali, F.W. Studier, S. Swaminathan. "Structural genomics: beyond the human genome project." Nat Genet 23, 151-157, 1999.

76. A. Sali, J. Kuriyan. "Challenges at the frontiers of structural biology (Reprinted from Trends in Biochemical Science, vol 12, Dec., 1999)." Trends Cell Biol 9, M20-M24, 1999.

77. A. Sali. "Functional links between proteins." Nature 402, 23, 25-26, 1999.

78. P. Baldi, M. Borodovsky, S. Brunak, C. Burge, J. Fickett, S. Henikoff, E. Koonin, A. Sali, C. Sander, G. Stormo. "The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function." Bioinformatics 15, 865-866, 1999.

79. C. Huang, G. Morales, A. Vagi, K. Chanasyk, M. Ferrazzi, C. Burklow, W.T. Qiu, E. Feyfant, A. Sali, R.L. Stevens. "Formation of enzymatically active, homotypic, and heterotypic tetramers of mouse mast cell tryptases. Dependence on a conserved Trp-rich domain on the surface." J Biol Chem 275, 351-358, 2000.

80. M.A. Marti-Renom, A.C. Stuart, A. Fiser, R. Sanchez, F. Melo, A. Sali. "Comparative protein structure modeling of genes and genomes." Annu Rev Biophys Biomol Struct 29, 291-325, 2000.

81. R. Sanchez, U. Pieper, N. Mirkovic, P.I.W. de Bakker, E. Wittenstein, A. Sali. "ModBase, a database of annotated comparative protein structure models." Nucleic Acids Res 28, 250-253, 2000.

82. A.R. Dinner, A. Sali, L.J. Smith, C.M. Dobson, M. Karplus. "Understanding protein folding via free-energy surfaces from theory and experiment." Trends Biochem Sci 25, 331-339, 2000.

83. R. Sanchez, A. Sali. "Comparative protein structure modeling. Introduction and practical examples with modeller." Methods Mol Biol 143, 97-129, 2000.

84. G. Wu, A.G. McArthur, A. Fiser, A. Sali, M.L. Sogin, M. Muller. "Core histones of the amitochondriate protist, Giardia lamblia." Mol Biol Evol 17, 1156-1163, 2000.

85. A. Fiser, R.K.G. Do, A. Sali. "Modeling of loops in protein structures." Protein Sci 9, 1753-1773, 2000.

86. W. Liedtke, Y. Choe, M.A. Marti-Renom, A.M. Bell, C.S. Denis, A. Sali, A.J. Hudspeth, J.M. Friedman, S. Heller. "Vanilloid receptor-related osmotically activated channel (VR-OAC), a candidate vertebrate osmoreceptor." Cell 103, 525-535, 2000.

87. S.K. Jin, S. Martinek, W.S. Joo, J.R. Wortman, N. Mirkovic, A. Sali, M.D. Yandell, N.P. Pavletich, M.W. Young, A.J. Levine. "Identification and characterization of a p53 homologue in Drosophila melanogaster." Proc Natl Acad Sci U S A 97, 7301-7306, 2000.

88. R. Sanchez, U. Pieper, F. Melo, N. Eswar, M.A. Marti-Renom, M.S. Madhusudhan, N. Mirkovic, A. Sali. "Protein structure modeling for structural genomics." Nat Struct Biol 7, 986-990, 2000.

89. A. Fiser, R. Sanchez, F. Melo, A. Sali. "Comparative protein structure modeling." In: Computational Biochemistry and Biophysics. Ed: M. Watanabe, B. Roux, A. Mackerell, O. Becker, pp. 275-312, Marcel Dekker, 2000.

90. C.M. Groft, R. Beckmann, A. Sali, S.K. Burley. "Crystal structures of ribosome anti-association factor IF6." Nat Struct Biol 7, 1156-1164, 2000.

91. S. Gopal, M. Schroeder, U. Pieper, A. Sczyrba, G. Aytekin-Kurban, S. Bekiranov, J.E. Fajardo, N. Eswar, R. Sanchez, A. Sali, T. Gaasterland. "Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome." Nat Genet 27, 337-340, 2001.

92. V.A. Eyrich, M.A. Marti-Renom, D. Przybylski, M.S. Madhusudhan, A. Fiser, F. Pazos, A. Valencia, A. Sali, B. Rost. "EVA: continuous automatic evaluation of protein structure prediction servers." Bioinformatics 17, 1242-1243, 2001.

93. M.A. Marti-Renom, V.A. Ilyin, A. Sali. "DBAli: a database of protein structure alignments." Bioinformatics 17, 746-747, 2001.

94. G.W. Wong, L. Li, M.S. Madhusudhan, S.A. Krilis, M.F. Gurish, M.E. Rothenberg, A. Sali, R.L. Stevens. "Tryptase 4, a new member of the chromosome 17 family of mouse serine proteases." J Biol Chem 276, 20648-20658, 2001.

95. L.G. Barrientos, R. Campos-Olivas, J.M. Louis, A. Fiser, A. Sali, A.M. Gronenborn. "1H, 13C, 15N resonance assignments and fold verification of a circular permuted variant of the potent HIV-inactivating protein cyanovirin-N." J Biomol NMR 19, 289-290, 2001.

96. A. Sali. "Target practice." Nat Struct Biol 8, 482-484, 2001.

97. J.B. Bonanno, C. Edo, N. Eswar, U. Pieper, M.J. Romanowski, V. Ilyin, S.E. Gerchman, H. Kycia, F.W. Studier, A. Sali, S.K. Burley. "Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis." Proc Natl Acad Sci U S A 98, 12896-12901, 2001.

98. C.M. Spahn, R. Beckmann, N. Eswar, P.A. Penczek, A. Sali, G. Blobel, J. Frank. "Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions." Cell 107, 373-386, 2001.

99. R. Beckmann, C.M.T. Spahn, N. Eswar, J. Helmers, P.A. Penczek, A. Sali, J. Frank, G. Blobel. "Architecture of the protein-conducting channel associated with the translating 80S ribosome." Cell 107, 361-372, 2001.

100. G.W. Wong, S. Yasuda, M.S. Madhusudhan, L. Li, Y. Yang, S.A. Krilis, A. Sali, R.L. Stevens. "Human tryptase epsilon (PRSS22), a new member of the chromosome 16p13.3 family of human serine proteases expressed in airway epithelial cells." J Biol Chem 276, 49169-49182, 2001.

101. M. Borodovsky, E. Koonin, C. Burge, J. Fickett, J. Logsdon, A. Sali, G. Stormo, I. Zhulin. "The third Georgia Tech - Emory international conference on bioinformatics: in silico biology; bioinformatics after human genome November 15-18, 2001, Atlanta, Georgia, USA." Bioinformatics 17, 859-861, 2001.

102. C.M. Groft, R. Beckmann, A. Sali, S.K. Burley. "Response to Paoli." Nat Struct Biol 8, 745, 2001.

103. D. Baker, A. Sali. "Protein structure prediction and structural genomics." Science 294, 93-96, 2001.

104. J. Vernal, A. Fiser, A. Sali, M. Muller, J.J. Cazzulo, C. Nowicki. "Probing the specificity of a trypanosomal aromatic alpha-hydroxy acid dehydrogenase by site-directed mutagenesis." Biochem Biophys Res Commun 293, 633-639, 2002.

105. F. Melo, R. Sanchez, A. Sali. "Statistical potentials for fold assessment." Protein Sci 11, 430-448, 2002.

106. A.C. Stuart, V.A. Ilyin, A. Sali. "LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures." Bioinformatics 18, 200-201, 2002.

107. M.A. Marti-Renom, M.S. Madhusudhan, A. Fiser, B. Rost, A. Sali. "Reliability of assessment of protein structure prediction methods." Structure 10, 435-440, 2002.

108. A. Sali, M.A. Marti-Renom, M.S. Madhusudhan, A. Fiser, B. Rost. "Reply to Moult et al." Structure 10, 292-293, 2002.

109. A. Fiser, M. Feig, C.L. Brooks, A. Sali. "Evolution and physics in comparative protein structure modeling." Accounts of Chemical Research 35, 413-421, 2002.

110. U. Pieper, N. Eswar, A.C. Stuart, V.A. Ilyin, A. Sali. "MODBASE, a database of annotated comparative protein structure models." Nucleic Acids Res 30, 255-259, 2002.

111. M.R. Chance, A.R. Bresnick, S.K. Burley, J.S. Jiang, C.D. Lima, A. Sali, S.C. Almo, J.B. Bonanno, J.A. Buglino, S. Boulton, H. Chen, N. Eswar, G.S. He, R. Huang, V. Ilyin, L. McMahan, U. Pieper, S. Ray, M. Vidal, L.K. Wang. "Structural genomics: A pipeline for providing structures for the biologist." Protein Sci 11, 723-738, 2002.

112. K.R. Rajashankar, M.R. Chance, S.K. Burley, J. Jiang, S.C. Almo, A.R. Bresnick, T. Dodatko, R. Huang, G. He, H. Chen, M. Sullivan, J. Toomey, R.A. Thirumuruhan, W.A. Franklin, A. Sali, U. Pieper, N. Eswar, V. Ilyin, L. McMahan. "Structural Genomics at the National Synchrotron Light Source." NSLS Activity Report 2001 2, 28-32, 2002.

113. Y. Yang, L.X. Li, G.W. Wong, S.A. Krilis, M.S. Madhusudhan, A. Sali, R.L. Stevens. "RasGRP4, a new mast cell-restricted Ras guanine nucleotide-releasing protein with calcium- and diacylglycerol-binding motifs - Identification of defective variants of this signaling protein in asthma, mastocytosis, and mast cell leukemia patients and demonstration of the importance of RasGRP4 in mast cell development and function." J Biol Chem 277, 25756-25774, 2002.

114. M.A. Marti-Renom, B. Yerkovich, A. Sali. "Comparative protein structure prediction." In: Current Protocols in Protein Science, pp. 2.9.1-2.9.22, John Wiley & Sons, 2002.

115. G.M. Iverson, S. Reddel, E.J. Victoria, K.A. Cockerill, Y.X. Wang, M.A. Marti-Renom, A. Sali, D.M. Marquis, S.A. Krilis, M.D. Linnik. "Use of single point mutations in domain I of beta(2)-glycoprotein I to determine fine antigenic specificity of antiphospholipid autoantibodies." J Immunol 169, 7097-7103, 2002.

116. A. Fiser, A. Sali. "Modeller: generation and refinement of homology-based protein structure models." Methods Enzymol 374, 461-491, 2003.

117. V.A. Ilyin, U. Pieper, A.C. Stuart, M.A. Marti-Renom, L. McMahan, A. Sali. "ModView, visualization of multiple protein sequences and structures." Bioinformatics 19, 165-166, 2003.

118. M.A. Marti-Renom, B. Yerkovich, A. Sali. "Modeling protein structure from its sequence." In: Current Protocols in Bioinformatics, V. 5 January Issue, pp. 5.1.1-5.1.32, John Wiley & Sons, Inc., Hoboken, NJ, 2003.

119. A. Fiser, A. Sali. "Comparative Protein Structure Modeling." In: Protein Structure. Ed: D. Chasman, pp. 167-206, Marcel Dekker, Inc., 2003.

120. A. Sali, R. Glaeser, T. Earnest, W. Baumeister. "From words to literature in structural proteomics." Nature 422, 216-225, 2003.

121. I.Y.Y. Koh, V.A. Eyrich, M.A. Marti-Renom, D. Przybylski, M.S. Madhusudhan, N. Eswar, O. Grana, F. Pazos, A. Valencia, A. Sali, B. Rost. "EVA: evaluation of protein structure prediction servers." Nucleic Acids Res 31, 3311-3315, 2003.

122. B. John, A. Sali. "Comparative protein structure modeling by iterative alignment, model building and model assessment." Nucleic Acids Res 31, 3982-3992, 2003.

123. N. Eswar, B. John, N. Mirkovic, A. Fiser, V.A. Ilyin, U. Pieper, A.C. Stuart, M.A. Marti-Renom, M.S. Madhusudhan, B. Yerkovich, A. Sali. "Tools for comparative protein structure modeling and analysis." Nucleic Acids Res 31, 3375-3380, 2003.

124. H.X. Gao, J. Sengupta, M. Valle, A. Korostelev, N. Eswar, S.M. Stagg, P. Van Roey, R.K. Agrawal, S.C. Harvey, A. Sali, M.S. Chapman, J. Frank. "Study of the structural dynamics of the E-coli 70S ribosome using real-space refinement." Cell 113, 789-801, 2003.

125. S.A. Lee, E.L. Shen, A. Fiser, A. Sali, S. Guo. "The zebrafish forkhead transcription factor Foxi1 specifies epibranchial placode-derived sensory neurons." Development 130, 2669-2679, 2003.

126. M.A. Marti-Renom, A. Fiser, M.S. Madhusudhan, B. John, A.C. Stuart, N. Eswar, U. Pieper, M.-.Y. Shen, A. Sali. "Modeling protein structure from its sequence." In: Current Protocols in Bioinformatics, V. 5, pp. 5.1.1-5.1.32, John Wiley & Sons, Inc., 2003.

127. A. Sali. "NIH workshop on structural proteomics of biological complexes." Structure 11, 1043-1047, 2003.

128. A. Fiser, A. Sali. "ModLoop: automated modeling of loops in protein structures." Bioinformatics 19, 2500-2501, 2003.

129. N. Mirkovic, M.A. Marti-Renom, B.L. Weber, A. Sali, A.N. Monteiro. "Structure-based assessment of missense mutations in human BRCA1: implications for breast and ovarian cancer predisposition." Cancer Res 64, 3790-3797, 2004.

130. A. Rossi, Q. Deveraux, B. Turk, A. Sali. "Comprehensive search for cysteine cathepsins in the human genome." Biol Chem 385, 363-372, 2004.

131. M.A. Marti-Renom, M.S. Madhusudhan, A. Sali. "Alignment of protein sequences by their profiles." Protein Sci 13, 1071-1087, 2004.

132. F. Alber, N. Eswar, A. Sali. "Structure determination of macromolecular complexes by experiment and computation." Practical Bioinformatics, Ed: J.Bujnicki 15, 73-96, 2004.

133. B. John, A. Sali. "Detection of homologous proteins by an intermediate sequence search." Protein Sci 13, 54-62, 2004.

134. S.M. Maurer, A. Rai, A. Sali. "Finding Cures for Tropical Diseases: Is Open Source An Answer?" Minnesota Journal of Law, Science & Technology 6, 169-175, 2004.

135. U. Pieper, N. Eswar, H. Braberg, M.S. Madhusudhan, F.P. Davis, A.C. Stuart, N. Mirkovic, A. Rossi, M.A. Marti-Renom, A. Fiser, B. Webb, D. Greenblatt, C.C. Huang, T.E. Ferrin, A. Sali. "MODBASE, a database of annotated comparative protein structure models, and associated resources." Nucleic Acids Res 32, D217-D222, 2004.

136. S.M. Maurer, A. Rai, A. Sali. "Finding Cures for Tropical Diseases: Is Open Source An Answer?" In: Biotechnology: Essays From Its Heartland. Ed: L.y.n.n. Laboratory Yarris, June 2004, pp. 33-37, 2004.

137. M.R. Chance, A. Fiser, A. Sali, U. Pieper, N. Eswar, G. Xu, J.E. Fajardo, T. Radhakannan, N. Marinkovic. "High-throughput computational and experimental techniques in structural genomics." Genome Res 14, 2145-2154, 2004.

138. M. Jacobson, A. Sali. "Comparative Protein Structure Modeling and Its Applications to Drug Discovery." In: Annual Reports in Medicinal Chemistry. Ed: J. Overington, 39, pp. 259-276, Inpharmatica Ltd., London, 2004.

139. R.B. Russell, F. Alber, P. Aloy, F.P. Davis, D. Korkin, M. Pichaud, M. Topf, A. Sali. "A structural perspective on protein-protein interactions." Curr Opin Struct Biol 14, 313-324, 2004.

140. D. Devos, S. Dokudovskaya, F. Alber, R. Williams, B.T. Chait, A. Sali, M.P. Rout. "Components of coated vesicles and nuclear pore complexes share a common molecular architecture." PLoS Biology 2, e380, 2004.

141. S.M. Maurer, A. Rai, A. Sali. "Finding Cures for Tropical Diseases: Is Open Source an Answer?" PLoS Medicine 1, e56, 2004.

142. J. Espadaler, R. Aragues, N. Eswar, M.A. Marti-Renom, E. Querol, F.X. Aviles, A. Sali, B. Oliva. "Detecting remotely related proteins by their interactions and sequence similarity." Proc Natl Acad Sci U S A 102, 7151-7156, 2005.

143. M. Topf, M.L. Baker, B. John, W. Chiu, A. Sali. "Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy." J Struct Biol 149, 191-203, 2005.

144. R. Karchin, L. Kelly, A. Sali. "Improving functional annotation of non-synonomous SNPs with information theory." Pac Symp Biocomput, 397-408, 2005.

145. M.S. Madhusudhan, M.A. Marti-Renom, N. Eswar, B. John, U. Pieper, R. Karchin, M.i.n.-.y.i. Shen, A. Sali. "Comparative Protein Structure Modeling." In: Proteomics Protocols Handbook. Ed: J.M. Walker, pp. 831-860, Humana Press Inc., Totowa, NJ, 2005.

146. F. Alber, M.F. Kim, A. Sali. "Structural characterization of assemblies from overall shape and subcomplex compositions." Structure 13, 435-445, 2005.

147. F.P. Davis, A. Sali. "PIBASE: a comprehensive database of structurally defined protein interfaces." Bioinformatics 21, 1901-1907, 2005.

148. R. Karchin, M. Diekhans, L. Kelly, D.J. Thomas, U. Pieper, N. Eswar, D. Haussler, A. Sali. "LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources." Bioinformatics 21, 2814-2820, 2005.

149. S. Yasuda, N. Morokawa, G.W. Wong, A. Rossi, M.S. Madhusudhan, A. Sali, Y.S. Askew, R. Adachi, G.A. Silverman, S.A. Krilis, R.L. Stevens. "Urokinase-type plasminogen activator is a preferred substrate of the human epithelium serine protease tryptase epsilon/PRSS22." Blood 105, 3893-3901, 2005.

150. J. Dvorak, M. Delcroix, A. Rossi, V. Vopalensky, M. Pospisek, M. Sedinova, L. Mikes, M. Sajid, A. Sali, J.H. Mckerrow, P. Horak, C.R. Caffrey. "Multiple cathepsin B isoforms in schistosomula of Trichobilharzia regenti: Identification, characterization and putative role in migration and nutrition." International Journal of Parasitology 35, 895-910, 2005.

151. A. Sali, W. Chiu. "Macromolecular assemblies highlighted." Structure 13, 339-341, 2005.

152. D. Korkin, F.P. Davis, A. Sali. "Localization of protein-binding sites within families of proteins." Protein Sci 14, 2350-2360, 2005.

153. M.Y. Shen, F.P. Davis, A. Sali. "The optimal size of a globular protein domain: A simple sphere-packing model." Chem Phys Lett 405, 224-228, 2005.

154. J.B. Bonanno, S.C. Almo, A. Bresnick, M.R. Chance, A. Fiser, S. Swaminathan, J. Jiang, F.W. Studier, L. Shapiro, C.D. Lima, T.M. Gaasterland, A. Sali, K. Bain, I. Feil, X. Gao, D. Lorimer, A. Ramos, J.M. Sauder, S.R. Wasserman, S. Emtage, K.L. D'Amico, S.K. Burley. "New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative." J Struct Funct Genom 6, 225-232, 2005.

155. M. Topf, A. Sali. "Combining electron microscopy and comparative protein structure modeling." Curr Opin Struct Biol 15, 578-585, 2005.

156. S.A. McMahon, J.L. Miller, J.A. Lawton, D.E. Kerkow, A. Hodes, M.A. Marti-Renom, S. Doulatov, E. Narayanan, A. Sali, J.F. Miller, P. Ghosh. "The C-type lectin fold as an evolutionary solution for massive sequence variation." Nature Structural Molecular Biology 12, 886-892, 2005.

157. D. Devos, S. Dokudovskaya, R. Williams, F. Alber, N. Eswar, B.T. Chait, M.P. Rout, A. Sali. "Simple fold composition and modular architecture of the nuclear pore complex." Proc Natl Acad Sci U S A 103, 2172-2177, 2006.

158. M.S. Madhusudhan, M.A. Marti-Renom, R. Sanchez, A. Sali. "Variable gap penalty for protein sequence-structure alignment." Protein Engineering, Design & Selection 19, 129-133, 2006.

159. C. Lima, J. Puglisi, A. Sali, L. Szewczak. "Editorial." Structure 14, 801, 2006.

160. U. Pieper, N. Eswar, F.P. Davis, H. Braberg, M.S. Madhusudhan, A. Rossi, M. Marti-Renom, R. Karchin, B.M. Webb, D. Eramian, M.Y. Shen, L. Kelly, F. Melo, A. Sali. "MODBASE: a database of annotated comparative protein structure models and associated resources." Nucleic Acids Res 34, D291-295, 2006.

161. M. Topf, M.L. Baker, M.A. Marti-Renom, W. Chiu, A. Sali. "Refinement of protein structures by iterative comparative modeling and CryoEM density fitting." J Mol Biol 357, 1655-1668, 2006.

162. D. Korkin, F.P. Davis, F. Alber, T. Luong, M.Y. Shen, V. Lucic, M.B. Kennedy, A. Sali. "Structural modeling of protein interactions by analogy: application to PSD-95." PLoS Computational Biology 2, e153, 2006.

163. D. Eramian, M.Y. Shen, D. Devos, F. Melo, A. Sali, M.A. Marti-Renom. "A composite score for predicting errors in protein structure models." Protein Sci 15, 1653-1666, 2006.

164. S. Dokudovskaya, R. Williams, D. Devos, A. Sali, B.T. Chait, M.P. Rout. "Protease accessibility laddering: a proteomic tool for probing protein structure." Structure 14, 653-660, 2006.

165. N. Eswar, B. Webb, M.A. Marti-Renom, M.S. Madhusudhan, D. Eramian, M.Y. Shen, U. Pieper, A. Sali. "Comparative protein structure modeling using Modeller." Curr Protoc Bioinformatics Chapter 5, Unit 5.6, 2006.

166. A. Rossi, M.A. Marti-Renom, A. Sali. "Localization of binding sites in protein structures by optimization of a composite scoring function." Protein Sci 15, 2366-2380, 2006.

167. F.P. Davis, H. Braberg, M.Y. Shen, U. Pieper, A. Sali, M.S. Madhusudhan. "Protein complex compositions predicted by structural similarity." Nucleic Acids Res 34, 2943-2952, 2006.

168. T.D. Nguyen, J.M. Gow, L.W. Chinn, L. Kelly, H. Jeong, C.C. Huang, D. Stryke, M. Kawamoto, S.J. Johns, E. Carlson, T. Taylor, T.E. Ferrin, A. Sali, K.M. Giacomini, D.L. Kroetz. "PharmGKB submission update: IV. PMT submissions of genetic variations in ATP-Binding cassette transporters to the PharmGKB network." Pharmacol Rev 58, 1-2, 2006.

169. H.M. Berman, S.K. Burley, W. Chiu, A. Sali, A. Adzhubei, P.E. Bourne, S.H. Bryant, R.L. Dunbrack Jr., K. Fidelis, J. Frank, A. Godzik, K. Henrick, A. Joachimiak, B. Heymann, D. Jones, J.L. Markley, J. Moult, G.T. Montelione, C. Orengo, M.G. Rossmann, B. Rost, H. Saibil, T. Schwede, D.M. Standley, J.D. Westbrook. "Outcome of a workshop on archiving structural models of biological macromolecules." Structure 14, 1211-1217, 2006.

170. A. Colubri, A.K. Jha, M.Y. Shen, A. Sali, R.S. Berry, T.R. Sosnick, K.F. Freed. "Minimalist representations and the importance of nearest neighbor effects in protein folding simulations." J Mol Biol 363, 835-857, 2006.

171. M.Y. Shen, A. Sali. "Statistical potential for assessment and prediction of protein structures." Protein Sci 15, 2507-2524, 2006.

172. N. Eswar, B. Webb, M.A. Marti-Renom, M.S. Madhusudhan, D. Eramian, M.Y. Shen, U. Pieper, A. Sali. "Comparative protein structure modeling using MODELLER." Curr Protoc Protein Sci Chapter 2, Unit 2.9, 2007.

173. R. Karchin, A.N. Monteiro, S.V. Tavtigian, M.A. Carvalho, A. Sali. "Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning." PLoS Computational Biology 3, e26, 2007.

174. L. Kelly, R. Karchin, A. Sali. "Protein interactions and disease phenotypes in the ABC transporter superfamily." Pac Symp Biocomput, 51-63, 2007.

175. N. Eswar, A. Sali. "Comparative Modeling of Drug Target Proteins." In: Volume 4 Computer-Assisted Drug Design, Comprehensive Medicinal Chemistry II. Ed: J. Taylor, D. Triggle, J.S. Mason, pp. 215-236, Elsevier Ltd, Oxford, UK, 2007.

176. M.A. Carvalho, S.M. Marsillac, R. Karchin, S. Manoukian, S. Grist, R.F. Swaby, T.P. Urmenyi, E. Rondinelli, R. Silva, L. Gayol, L. Baumbach, R. Sutphen, J.L. Pickard-Brzosowicz, K.L. Nathanson, A. Sali, D. Goldgar, F.J. Couch, P. Radice, A.N. Monteiro. "Determination of cancer risk associated with germ line BRCA1 missense variants by functional analysis." Cancer Res 67, 1494-1501, 2007.

177. S.X. Wang, K.C. Pandey, J. Scharfstein, J. Whisstock, R.K. Huang, J. Jacobelli, R.J. Fletterick, P.J. Rosenthal, M. Abrahamson, L.S. Brinen, A. Rossi, A. Sali, J.H. McKerrow. "The structure of chagasin in complex with a cysteine protease clarifies the binding mode and evolution of an inhibitor family." Structure 15, 535-543, 2007.

178. E. Feyfant, A. Sali, A. Fiser. "Modeling mutations in protein structures." Protein Sci 16, 2030-2041, 2007.

179. N. Soranzo, L. Kelly, L. Martinian, M.W. Burley, M. Thom, A. Sali, D.L. Kroetz, D.B. Goldstein, S.M. Sisodiya. "Lack of support for a role for RLIP76 (RALBP1) in response to treatment or predisposition to epilepsy." Epilepsia 48, 674-683, 2007.

180. K. Bajaj, M.S. Madhusudhan, B.V. Adkar, P. Chakrabarti, C. Ramakrishnan, A. Sali, R. Varadarajan. "Stereochemical criteria for prediction of the effects of proline mutations on protein stability." PLoS Comput Biol 3, e241, 2007.

181. R. Aragues, A. Sali, J. Bonet, M.A. Marti-Renom, B. Oliva. "Characterization of protein hubs by inferring interacting motifs from protein interactions." PLoS Comput Biol 3, 1761-1771, 2007.

182. M.A. Marti-Renom, A. Rossi, F. Al-Shahrour, F.P. Davis, U. Pieper, J. Dopazo, A. Sali. "The AnnoLite and AnnoLyze programs for comparative annotation of protein structures." BMC Bioinformatics 8 Suppl 4, S4, 2007.

183. M.A. Marti-Renom, U. Pieper, M.S. Madhusudhan, A. Rossi, N. Eswar, F.P. Davis, F. Al-Shahrour, J. Dopazo, A. Sali. "DBAli tools: mining the protein structure space." Nucleic Acids Res 35, W393-397, 2007.

184. F.P. Davis, D.T. Barkan, N. Eswar, J.H. McKerrow, A. Sali. "Host pathogen protein interactions predicted by comparative modeling." Protein Sci 16, 2585-2596, 2007.

185. S.C. Almo, J.B. Bonanno, J.M. Sauder, S. Emtage, T.P. Dilorenzo, V. Malashkevich, S.R. Wasserman, S. Swaminathan, S. Eswaramoorthy, R. Agarwal, D. Kumaran, M. Madegowda, S. Ragumani, Y. Patskovsky, J. Alvarado, U.A. Ramagopal, J. Faber-Barata, M.R. Chance, A. Sali, A. Fiser, Z.Y. Zhang, D.S. Lawrence, S.K. Burley. "Structural genomics of protein phosphatases." J Struct Funct Genom 8, 121-140, 2007.

186. F. Melo, A. Sali. "Fold assessment for comparative protein structure modeling." Protein Sci 16, 2412-2426, 2007.

187. A. Sali, C.D. Lima, M. Kostic. "Structural genomics." Structure 15, 1341, 2007.

188. V.D. Winn, R. Haimov-Kochman, A.C. Paquet, Y.J. Yang, M.S. Madhusudhan, M. Gormley, K.T. Feng, D.A. Bernlohr, S. McDonagh, L. Pereira, A. Sali, S.J. Fisher. "Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term." Endocrinology 148, 1059-1079, 2007.

189. C.V. Robinson, A. Sali, W. Baumeister. "The molecular sociology of the cell." Nature 450, 973-982, 2007.

190. F. Alber, S. Dokudovskaya, L.M. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, B.T. Chait, A. Sali, M.P. Rout. "The molecular architecture of the nuclear pore complex." Nature 450, 695-701, 2007.

191. F. Alber, S. Dokudovskaya, L.M. Veenhoff, W. Zhang, J. Kipper, D. Devos, A. Suprapto, O. Karni-Schmidt, R. Williams, B.T. Chait, M.P. Rout, A. Sali. "Determining the architectures of macromolecular assemblies." Nature 450, 683-694, 2007.

192. N. Eswar, D. Eramian, B. Webb, M.Y. Shen, A. Sali. "Protein structure modeling with MODELLER." Methods Mol Biol 426, 145-159, 2008.

193. T. Schwede, A. Sali, N. Eswar, M.C. Peitsch. "Protein Structure Modeling." In: Computational Structural Biology. Ed: T. Schwede, M.C. Peitsch, pp. 3-35, World Scientific Publishing Ltd., Singapore, 2008.

194. Y. Cong, M. Topf, A. Sali, P. Matsudaira, M. Dougherty, W. Chiu, M.F. Schmid. "Crystallographic conformers of actin in a biologically active bundle of filaments." J Mol Biol 375, 331-336, 2008.

195. C.R. Booth, A.S. Meyer, Y. Cong, M. Topf, A. Sali, S.J. Ludtke, W. Chiu, J. Frydman. "Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT." Nat Struct Mol Biol 15, 746-753, 2008.

196. S.K. Burley, S.C. Almo, J.B. Bonanno, M.R. Chance, S. Emtage, A. Fiser, A. Sali, J.M. Sauder, S. Swaminathan. "Structure Genomics of Protein Superfamilies." In: Structural Bioinformatics, 2nd Edition. Ed: J. Gu, P.E. Bourne, Wiley-Blackwell, New York, NY, 2008.

197. F. Alber, B.T. Chait, M.P. Rout, A. Sali. "Integrative Structure Determination of Protein Assemblies by Satisfaction of Spatial Restraints." In: Protein-protein interactions and networks: identification, characterization and prediction. Ed: A. Panchenko, T. Przytycka, pp. 99-114, Springer-Verlag, London, UK, 2008.

198. P. Chandramouli, M. Topf, J.F. Menetret, N. Eswar, J.J. Cannone, R.R. Gutell, A. Sali, C.W. Akey. "Structure of the mammalian 80S ribosome at 8.7 A resolution." Structure 16, 535-548, 2008.

199. F. Alber, F. Forster, D. Korkin, M. Topf, A. Sali. "Integrating diverse data for structure determination of macromolecular assemblies." Annu Rev Biochem 77, 443-477, 2008.

200. M. Topf, K. Lasker, B. Webb, H. Wolfson, W. Chiu, A. Sali. "Protein structure fitting and refinement guided by cryo-EM density." Structure 16, 295-307, 2008.

201. J. Espadaler, N. Eswar, E. Querol, F.X. Aviles, A. Sali, M.A. Marti-Renom, B. Oliva. "Prediction of enzyme function by combining sequence similarity and protein interactions." BMC Bioinformatics 9, 249, 2008.

202. F. Aguero, B. Al-Lazikani, M. Aslett, M. Berriman, F.S. Buckner, R.K. Campbell, S. Carmona, I.M. Carruthers, A.W. Chan, F. Chen, G.J. Crowther, M.A. Doyle, C. Hertz-Fowler, A.L. Hopkins, G. McAllister, S. Nwaka, J.P. Overington, A. Pain, G.V. Paolini, U. Pieper, S.A. Ralph, A. Riechers, D.S. Roos, A. Sali, D. Shanmugam, T. Suzuki, W.C. Van Voorhis, C.L. Verlinde. "Genomic-scale prioritization of drug targets: the TDR Targets database." Nat Rev Drug Discov 7, 900-907, 2008.

203. R. Karchin, M. Agarwal, A. Sali, F. Couch, M.S. Beattie. "Classifying Variants of Undetermined Significance in BRCA2 with Protein Likelihood Ratios." Cancer Inform 6, 203-216, 2008.

204. K.A. Krukenberg, F. Forster, L.M. Rice, A. Sali, D.A. Agard. "Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90." Structure 16, 755-765, 2008.

205. D. Eramian, N. Eswar, M.Y. Shen, A. Sali. "How well can the accuracy of comparative protein structure models be predicted?" Protein Sci 17, 1881-1893, 2008.

206. F. Forster, B. Webb, K.A. Krukenberg, H. Tsuruta, D.A. Agard, A. Sali. "Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies." J Mol Biol 382, 1089-1106, 2008.

207. C.M. Anderson, D. Korkin, D.L. Smith, S. Makovets, J.J. Seidel, A. Sali, E.H. Blackburn. "Tel2 mediates activation and localization of ATM/Tel1 kinase to a double-strand break." Genes Dev 22, 854-859, 2008.

208. R.A. Chiang, A. Sali, P.C. Babbitt. "Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies." PLoS Comput Biol 4, e1000142, 2008.

209. S. Mahrus, J.C. Trinidad, D.T. Barkan, A. Sali, A.L. Burlingame, J.A. Wells. "Global Sequencing of Proteolytic Cleavage Sites in Apoptosis by Specific Labeling of Protein N Termini." Cell 134, 866-876, 2008.

210. I.I. Serysheva, S.J. Ludtke, M.L. Baker, Y. Cong, M. Topf, D. Eramian, A. Sali, S.L. Hamilton, W. Chiu. "Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel." Proc Natl Acad Sci U S A 105, 9610-9615, 2008.

211. S. Graslund, P. Nordlund, J. Weigelt, B.M. Hallberg, J. Bray, O. Gileadi, S. Knapp, U. Oppermann, C. Arrowsmith, R. Hui, J. Ming, S. dhe-Paganon, H. Park, A. Savchenko, A. Yee, A. Edwards, R. Vincentelli, C. Cambillau, R. Kim, S. Kim, Z. Rao, Y. Shi, T.C. Terwilliger, C. Kim, L. Hung, G.S. Waldo, Y. Peleg, S. Albeck, T. Unger, O. Dym, J. Prilusky, J.L. Sussman, R.C. Stevens, S.A. Lesley, I.A. Wilson, A. Joachimiak, F. Collart, I. Dementieva, M.I. Donnelly, W.H. Eschenfeldt, Y. Kim, L. Stols, R. Wu, M. Zhou, S.K. Burley, J.S. Emtage, J.M. Sauder, D. Thompson, K. Bain, J. Luz, T. Gheyi, F. Zhang, S. Atwell, S.C. Almo, J.B. Bonanno, A. Fiser, S. Swaminathan, F.W. Studier, M.R. Chance, A. Sali, T.B. Acton, R. Xiao, L. Zhao, L.C. Ma, J.F. Hunt, L. Tong, K. Cunningham, M. Inouye, S. Anderson, H. Janjua, R. Shastry, C.K. Ho, D. Wang, H. Wang, M. Jiang, G.T. Montelione, D.I. Stuart, R.J. Owens, S. Daenke, A. Schutz, U. Heinemann, S. Yokoyama, K. Bussow, K.C. Gunsalus. "Protein production and purification (vol 5, pg 135, 2008)." Nat Methods 5, 369-369, 2008.

212. N. Eswar, A. Sali. "Protein Structure Modeling." In: From Molecules to Medicine, Structure of Biological Macromolecules and Its Relevance in Combating New Diseases and Bioterrorism. Ed: J.L. Sussman, P. Spadon, pp. 139-151, Springer-Verlag, Dordrecht, The Netherlands, 2009.

213. U. Pieper, R. Chiang, J.J. Seffernick, S.D. Brown, M.E. Glasner, L. Kelly, N. Eswar, J.M. Sauder, J.B. Bonanno, S. Swaminathan, S.K. Burley, X. Zheng, M.R. Chance, S.C. Almo, J.A. Gerlt, F.M. Raushel, M.P. Jacobson, P.C. Babbitt, A. Sali. "Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies." J Struct Funct Genom 10, 107-125, 2009.

214. U. Pieper, N. Eswar, B.M. Webb, D. Eramian, L. Kelly, D.T. Barkan, H. Carter, P. Mankoo, R. Karchin, M.A. Marti-Renom, F.P. Davis, A. Sali. "MODBASE, a database of annotated comparative protein structure models and associated resources." Nucleic Acids Res 37, D347-354, 2009.

215. F.A. Hays, Z. Roe-Zurz, M. Li, L. Kelly, F. Gruswitz, A. Sali, R.M. Stroud. "Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination." J Struct Funct Genom 10, 9-16, 2009.

216. M. Li, F.A. Hays, Z. Roe-Zurz, L. Vuong, L. Kelly, C.M. Ho, R.M. Robbins, U. Pieper, J.D. O'Connell 3rd, L.J. Miercke, K.M. Giacomini, A. Sali, R.M. Stroud. "Selecting optimum eukaryotic integral membrane proteins for structure determination by rapid expression and solubilization screening." J Mol Biol 385, 820-830, 2009.

217. M.E. Peterson, F. Chen, J.G. Saven, D.S. Roos, P.C. Babbitt, A. Sali. "Evolutionary constraints on structural similarity in orthologs and paralogs." Protein Sci 18, 1306-1315, 2009.

218. D. Russel, K. Lasker, J. Phillips, D. Schneidman-Duhovny, J.A. Velazquez-Muriel, A. Sali. "The structural dynamics of macromolecular processes." Curr Opin Cell Biol 21, 97-108, 2009.

219. T. Schwede, A. Sali, B. Honig, M. Levitt, H.M. Berman, D. Jones, S.E. Brenner, S.K. Burley, R. Das, N.V. Dokholyan, R.L. Dunbrack Jr, K. Fidelis, A. Fiser, A. Godzik, Y.J. Huang, C. Humblet, M.P. Jacobson, A. Joachimiak, S.R. Krystek Jr, T. Kortemme, A. Kryshtafovych, G.T. Montelione, J. Moult, D. Murray, R. Sanchez, T.R. Sosnick, D.M. Standley, T. Stouch, S. Vajda, M. Vasquez, J.D. Westbrook, I.A. Wilson. "Outcome of a workshop on applications of protein models in biomedical research." Structure 17, 151-159, 2009.

220. L. Orti, R.J. Carbajo, U. Pieper, N. Eswar, S.M. Maurer, A.K. Rai, G. Taylor, M.H. Todd, A. Pineda-Lucena, A. Sali, M.A. Marti-Renom. "A kernel for open source drug discovery in tropical diseases." PLoS Negl Trop Dis 3, e418, 2009.

221. K.C. Pandey, D.T. Barkan, A. Sali, P.J. Rosenthal. "Regulatory elements within the prodomain of falcipain-2, a cysteine protease of the malaria parasite Plasmodium falciparum." PLoS One 4(5):e5694, 2009.

222. R.M. Stroud, S. Choe, J. Holton, H.R. Kaback, W. Kwiatkowski, D.L. Minor, R. Riek, A. Sali, H. Stahlberg, W. Harries. "2007 Annual progress report synopsis of the Center for Structures of Membrane Proteins." J Struct Funct Genom 10, 193-208, 2009.

223. L. Orti, R.J. Carbajo, U. Pieper, N. Eswar, S.M. Maurer, A.K. Rai, G. Taylor, M.H. Todd, A. Pineda-Lucena, A. Sali, M.A. Marti-Renom. "A kernel for the Tropical Disease Initiative." Nat Biotechnol 27, 320-321, 2009.

224. O. Fornes, R. Aragues, J. Espadaler, M.A. Marti-Renom, A. Sali, B. Oliva. "ModLink+: Improving fold recognition by using protein-protein interactions." Bioinformatics 25, 1506-1512, 2009.

225. S. Nickell, F. Beck, S.H.W. Scheres, A. Korinek, F. Forster, K. Lasker, O. Mihalache, N. Sun, I. Nagy, A. Sali, J. Plitzko, J.-M. Carazo, M. Mann, W. Baumeister. "Insights into the Molecular Architecture of the 26S Proteasome." Proc Natl Acad Sci U S A 29, 11943-11947, 2009.

226. K. Lasker, M. Topf, A. Sali, H.J. Wolfson. "Inferential optimization for simultaneous fitting of multiple components into a cryoEM map of their assembly." J Mol Biol 388, 180-194, 2009.

227. M.S. Madhusudhan, B.M. Webb, M.A. Marti-Renom, N. Eswar, A. Sali. "Alignment of multiple protein structures based on sequence and structure features." Protein Eng Des Sel 22, 569-574, 2009.

228. J.A. DeGrasse, K.N. DuBois, D. Devos, T.N. Siegel, A. Sali, M.C. Field, M.P. Rout, B.T. Chait. "The Establishment of Nuclear Pore Complex Architecture Occurred Early in Evolution." Mol Cell Proteomics 8, 2119-2130, 2009.

229. L. Kelly, U. Pieper, N. Eswar, F.A. Hays, M. Li, Z. Roe-Zurz, D. Kroetz, K.M. Giacomini, R.M. Stroud, A. Sali. "A survey of integral alpha-helical membrane proteins." J Struct Funct Genomics 10, 269-280, 2009.

230. T. Lezon, A. Sali, I. Bahar. "Global motions of the nuclear pore complex:Insights from Elastic Network Models." PLoS Comp Biol 5, e1000496, 2009.

231. D.J. Taylor, B. Devkota, A.D. Huang, M. Topf, N. Eswar, A. Sali, S.C. Harvey, J. Frank. "Comprehensive Molecular Structure of the Eukaryotic Ribosome." Structure 17, 1591-1604, 2009.

232. H. Fan, J.J. Irwin, B.M. Webb, G. Klebe, B. Shoichet, A. Sali. "Molecular Docking Screens Using Comparative Models of Proteins." J Chem Inf Model 49, 2512-2527, 2009.

233. F. Forster, K. Lasker, F. Beck, S. Nickell, A. Sali, W. Baumeister. "An Atomic Model AAA-ATPase/20S core particle sub-complex of the 26S proteasome." Biochem Biophys Res Commun 388, 228-233, 2009.

234. D. Kroetz, N. Ahituv, E. Burchard, S. Guo, A. Sali, K. Giacomini. "The Pharmacogenomics Center of the University of California, Sam Francisco: At the interface of genomics, biological mechanism and drug therapy." Pharmacogenomics 10, 1569-1576, 2009.

235. F.P. Davis, A. Sali. "The overlap of small molecule and protein binding sites within families of protein structures." PLoS Comp Biol 6, e1000668, 2010.

236. D. Barkan, D. Hostetter, S. Mahrus, U. Pieper, J. Wells, C. Craik, A. Sali. "Prediction of Protease Substrates using Sequence and Structure Features." Bioinformatics 26, 1714-1722, 2010.

237. F. Gruswitz, S. Chaudhary, J. Ho, A. Schlessinger, P. Bobak, C. Ho, A. Sali, C. Westhoff, R. Stroud. "Function of Human Rh based on Structure of RhCG at 2.1 Å." Proc Natl Acad Sci U S A 107, 9638-9643, 2010.

238. L. Chen, B. Pawlikowski, A. Schlessinger, S. More, D. Stryke, S.J. Johns, M. Portman, T.E. Ferrin, A. Sali, K. Giacomini. "Role of organic cation transporter 3 (SLC22A3) and Its missense variants in the pharmacologic action of metformin." Pharmacogenet Genomics 20, 687-699, 2010.

239. A. Schlessinger, P. Matsson, J.E. Shima, U. Pieper, S.W. Yee, L. Kelly, L. Apeltsin, R.M. Stroud, T.E. Ferrin, K.M. Giacomini, A. Sali. "Comparison of Human Solute Carriers." Protein Sci 19, 412-428, 2010.

240. D. Schneidman-Duhovny, M. Hammel, A. Sali. "FoXS: A Web Server for Rapid Computation and Fitting of SAXS Profiles." Nucleic Acids Res 38, 541-544, 2010.

241. K. Lasker, J.L. Phillips, D. Russel, J. Velazquez-Muriel, D. Schneidman-Duhovny, B. Webb, A. Schlessinger, A. Sali. "Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data." Mol Cell Proteomics 9, 1689-1702, 2010.

242. P. Sampathkumar, S.A. Ozyurt, J. Do, K.T. Bain, M. Dickey, L.A. Rodgers, T. Gheyi, A. Sali, S.J. Kim, J. Phillips, U. Pieper, J. Fernandez-Martinez, J.D. Franke, A. Martel, H. Tsuruta, S. Atwell, D.A. Thompson, J.S. Emtage, S.R. Wasserman, M.P. Rout, J.M. Sauder, S.K. Burley. "Structures of the autoproteolytic domain from the Saccharomyces cerevisiae nuclear pore complex component, Nup 145." Proteins:Struct Funct Bioinform 78, 1992-1998, 2010.

243. P. Sampathkumar, F. Lu, X. Zhao, Z. Li, J. Gilmore, K. Bain, M.E. Rutter, T. Gheyi, K. Schwinn, J. Bonanno, U. Pieper, J.E. Fajardo, A. Fiser, S. Almo, A. Swaminathan, M. Chance, D. Baker, S. Atwell, D. Thompson, J.S. Emtage, S. Wasserman, A. Sali, J.M. Sauder, S. Burley. "Structure of a putative BenF-like porin from Pseudomanas fluorescens Pf-5 at 2.6 Å resolution." Proteins:Struct Funct Bioinform 78, 3056-3062, 2010.

244. K. Lasker, A. Sali, H.J. Wolfson. "Determining macromolecular assembly structures by molecular docking and fitting into an electron density map." Proteins:Struct Funct Bioinform 78, 3205-3211, 2010.

245. L. Chen, M. Takizawa, E. Chen, A. Schlessinger, J.H. Choi, J. Segenthelar, A. Sali, M. Kubo, S. Nakamura, Y. Iwamoto, N. Iwasaki, K.M. Giacomini. "Genetic polymorphisms in the organic cation transporter 1, OCT1, in Chinese and Japanese populations, exhibit altered function." J Pharmacol Exp Ther 1, 42-50, 2010.

246. L. Kelly, H. Fukushima, R. Karchin, J.M. Gow, L.W. Chinn, U. Pieper, M.R. Segal, D.L. Kroetz, A. Sali. "Functional Hot Spots in Human ATP-binding Cassette Transporter Nucleotide Binding Domains." Protein Sci 19, 2110-2121, 2010.

247. F. Forster, K. Lasker, S. Nickell, A. Sali, W. Baumeister. "Toward an integrated structural model of the 26S proteasome." Mol Cell Proteomics 9, 1666-1677, 2010.

248. D. Schneidman-Duhovny, M. Hammel, A. Sali. "Macromolecular docking restrained by a small angle X-ray scattering profile." J Struct Biol 3, 461-471, 2011.

249. L. Kelly, H. Fukushima, R. Karchin, J.M. Gow, L.W. Chinn, U. Pieper, M.R. Segal, D.L. Kroetz, A. Sali. "Response to "Predictable difficulty or difficulty to predict" by Tamas Aranyi, Krisztina Fulop, Orsolya Symmons, Viola Pomozi, and Andras Varadi." Protein Sci 20, 4-5, 2011.

250. U. Pieper, B.M. Webb, D.T. Barkan, D. Schneidman-Duhovny, A. Schlessinger, H. Braberg, Z. Yang, E.C. Meng, E.F. Pettersen, C.C. Huang, R.S. Datta, P. Sampathkumar, M.S. Madhusudhan, K. Sjolander, T.E. Ferrin, S.K. Burley, A. Sali. "ModBase, a database of annotated comparative protein structure models, and associated resources." Nucleic Acids Res 39, 465-474, 2011.

251. S.S. Kamat, A. Bagaria, D. Kumaran, G.P. Holmes-Hampton, H. Fan, A. Sali, J.M. Sauder, S.K. Burley, P.A. Lindahl, S. Swaminathan, F.M. Raushel. "Catalytic Mechanism and Three-Dimensional Structure of Adenine Deaminase." Biochemistry 50, 1917-1927, 2011.

252. B. Webb, K. Lasker, D. Schneidman-Duhovny, E. Tjioe, J. Phillips, S.J. Kim, J. Velazquez-Muriel, D. Russel, A. Sali. "Modeling of Proteins and their Assemblies with the Integrative Modeling Platform." In: Methods in Molecular Biology, pp. 377-397, Humana Press, 2011.

253. P. Sampathkumar, T. Gheyi, S.A. Miller, K.T. Bain, M. Dickey, J.B. Bonanno, Kim. S.J., J. Phillips, U. Pieper, J. Fernandez-Martinez, J. Franke, A. Martel, H. Tsuruta, S. Atwell, D.A. Thompson, J.S. Emtage, S.R. Wasserman, M.P. Rout, A. Sali, J.M. Sauder, S.K. Burley. "Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the Nuclear Pore Complex." Proteins:Struct Funct Bioinform 79, 1672-1677, 2011.

254. S.S. Kamat, H. Fan, J.M. Sauder, S.K. Burley, B.K. Shoichet, A. Sali, F.M. Raushel. "Enzymatic deamination of the epigenetic base N-6-methyladenine." J Am Chem Soc 133, 2080-2083, 2011.

255. S. Dokudovskaya, F. Waharte, A. Schlessinger, U. Pieper, D.P. Devos, I.M. Cristea, R. Williams, J. Salamero, B.T. Chait, A. Sali, M.C. Field, M.C. Rout, C. Dargemont. "A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae." Mol Cell Proteomics 10, M110.006478, 2011.

256. M. Field, A. Sali, M. Rout. "On a bender: Bars, ESCRTs, COPs, and finally getting your coat." J Cell Biol 193, 963-972, 2011.

257. H. Fan, D. Schneidman, J.J. Irwin, G. Dong, B. Shoichet, A. Sali. "Statistical Potential for Modeling and Ranking Protein-Ligand Interactions." J Chem Inf Model 51, 3078-3092, 2011.

258. S. Jager, P. Cimermancic, N. Gulbahce, J. Johnson, K. McGovern, S. Clarke, M. Shales, G. Mercenne, K. Li, H. Barry, G. Jang, E. Akiva, L. Pache, J. Marlett, S. Roth, M. Stephens, I. D’Orso, J. Fernandes, M. Fahey, C. Mahon, A. O’Donoghue, A. Todorovic, J. Morris, D. Maltby, T. Alber, G. Cagney, F. Bushman, J. Young, S. Chanda, W. Sundquist, T. Kortemme, R. Hernandez, C. Craik, A. Burlingame, A. Sali, A. Frankel, N. Krogan. "Global Landscape of HIV-Human Protein Complexes." Nature 481, 365-370, 2011.

259. S. Jager, D.Y. Kim, K. Shindo, E. Kwon, R. LaRue, C. Mahon, P. Cimermancic, L. Yen, D. Stanley, M. Li, A. Burlingame, A. Sali, C. Craik, R. Harris, J. Gross, N. Krogan. "Vif Hijacks CBFβ to Degrade APOBEC3G and Promote HIV-1 Infection." Nature 481, 371-375, 2011.

260. E. Tjioe, K. Lasker, B. Webb, H. Wolfson, A. Sali. "MultiFit: A web server for fitting multiple protein structures into their electron microscopy density map." Nucleic Acids Res 39, 167-170, 2011.

261. J. Carlsson, R. Coleman, V. Setola, J. Irwin, H. Fan, A. Schlessinger, A. Sali, B. Roth, B. Shoichet. "Structure-based Ligand Discovery Against a Homology Model and X-ray Structure of the Dopamine D3 Receptor." Nat Chem Biol 7, 769-778, 2011.

262. A. Schlessinger, E. Geier, H. Fan, J. Irwin, B. Shoichet, K. Giacomini, A. Sali. "Structure-based Discovery of Prescription Drugs that Interact with the Norepinephrine Transporter, NET." Proc Natl Acad Sci USA 108, 15810-15815, 2011.

263. J. Choi, S. Yee, A. Ramirez, K. Morrissey, G. Jang, P. Joski, J. Mefford, S. Hesselson, A. Schlessinger, G. Jenkins, R. Castro, S. Johns, D. Stryke, A. Sali, T. Ferrin, J. Witte, P. Kwok, D. Roden, R. Wilke, C. McCarty, R. Davis, K. Giacomini. "A Common Promoter Variant in MATE2-K Is Associated with Poor Response to Metformin." Clin Pharmacol Ther 90, 674-684, 2011.

264. A.M. Goble, H. Fan, A. Sali, F.M. Raushel. "Discovery of a Cytokinin Deaminase." ACS Chem Biol 6, 1036-1040, 2011.

265. J. Gerlt, K. Allen, S. Almo, R. Armstrong, P. Babbitt, J. Cronan, D. Dunaway-Mariano, H. Imker, M. Jacobson, W. Minor, C. Poulter, F. Raushel, A. Sali, B. Shoichet, J. Sweedler. "The Enzyme Function Initiative." Biochemistry 50, 9950-9962, 2011.

266. Z. Yang, K. Lasker, D. Schneidman-Duhovny, B. Webb, C. Huang, E. Pettersen, T. Goddard, E. Meng, A. Sali, T. Ferrin. "UCSF Chimera, MODELLER, and IMP: an integrated Modeling System." J Struct Biol 179, 269-278, 2012.

267. K. Lasker, J. Velazquez-Muriel, B. Webb, Z. Yang, T.E. Ferrin, A. Sali. "Macromolecular assembly structures by comparative modeling and electron microscopy." In: Methods in Molecular Biology. Ed: J. Walker, pp. 331-350, Humana Press, New York, NY, 2012.

268. H. Fan, J. Irwin, A. Sali. "Virtual Ligand Screening Against Comparative Protein Structure Models." Methods Mol Biol 819, 105-126, 2012.

269. J. Fernandez-Martinez, J. Phillips, M. Sekedat, R. Diaz-Avalos, J. Velazquez-Muriel, J. Franke, R. Williams, D. Stokes, B. Chait, A. Sali, M. Rout. "Structure-function Map for a Heptameric Component of the Nuclear Pore Complex." J Cell Biol 196, 419-434, 2012.

270. R. Henderson, A. Sali, M. Baker, B. Carragher, B. Devkota, K. Downing, E. Egelman, Z. Feng, J. Frank, N. Grigorieff, W. Jiang, S. Ludtke, O. Medalia, P. Penczek, P. Rosenthal, M. Rossmann, M. Schmid, G. Schroder, A. Steven, D. Stokes, J. Westbrook, W. Wriggers, H. Yang, J. Young, H. Berman, W. Chiu, G. Kleywegt, C. Lawson. "Outcome of the First Electron Microscopy Validation Task Force Meeting." Structure 20, 205-214, 2012.

271. P. Weinkam, J. Pons, A. Sali. "Structure-based Model of Allostery Predicts Coupling Between Distant Sites." Proc Natl Acad Sci USA 109, 4875-4880, 2012.

272. D. Russel, K. Lasker, B. Webb, J. Velazquez-Muriel, E. Tjioe, D. Schneidman-Duhovny, B. Peterson, A. Sali. "Putting the pieces together: integrative structure determination of macromolecular assemblies." PLoS Biol 10, e1001244, 2012.

273. G. Pathare, I. Nagy, S. Bohn, P. Unverdorben, A. Hubert, R. Korner, S. Nickell, K. Lasker, A. Sali, T. Tamura, T. Nishioka, F. Forster, W. Baumeister, A. Bracher. "The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together." Proc Natl Acad Sci USA 109, 149-154, 2012.

275. P. Sampathkumar, S.J. Kim, D. Manglicmot, K.T. Bain, J. Gilmore, T. Gheyi, J. Phillips, U. Pieper, J. Fernandez-Martinez, J. Franke, T. Matsui, H. Tsuruta, S. Atwell, D. Thompson, J.S. Emtage, S. Wasserman, M. Rout, A. Sali, J.M. Sauder, S.C. Almo, S.K. Burley. "Atomic structure of the Nuclear Pore Complex targeting domain of Nup116 homologue from the yeast, Candida glabrata." Proteins:Struct Funct Bioinform 8, 2110-2116, 2012.

276. C. Klammt, I. Maslennikov, M. Bayrhuber, C. Eichmann, N. Vajpai, E. Chiu, K. Blain, L. Esquivies, H. Kwon, B. Balana, U. Pieper, A. Sali, P. Slesinger, W. Kwiatkowski, R. Rick, S. Choe. "Facile Backbone structure determination of human membrane proteins by NMR spectroscopy." Nat Methods 8, 834-839, 2012.

277. D. Schneidman-Duhovny, A. Rossi, A. Avila-Sakar, S.J. Kim, J. Velazquez-Muriel, P. Strop, H. Liang, K.A. Krukenberg, M. Liao, H.M. Kim, S. Sobhanifar, V. Dotsch, A. Raipal, J. Pons, D.A. Agard, Y. Cheng, A. Sali. "A Method for Integrative Structure Determination of Protein-Protein Complexes." Bioinformatics 28, 3282-3289, 2012.

278. V. Puizdar, T. Zajc, E. Zerovnik, M. Renko, U. Pieper, N. Eswar, A. Sali, I. Dolenc, V. Turk. "Biochemical Characterization and Structural Modeling of Human Cathepsin E Variant 2 in Comparison to the Wild-type Protein." Biol Chem 393, 177-186, 2012.

286. A. Schlessinger, M.B. Wittwer, A. Dahlin, N. Khuri, M. Bonomi, H. Fan, K. Giacomini, A. Sali. "High Selectivity of the γ-Aminobutyric Acid Transporter 2 (GAT-2, SLC6A13) Revealed by Structure-based Approach." J Biol Chem 287, 37745-37756, 2012.

287. D. Schneidman-Duhovny, S.J. Kim, A. Sali. "Integrative structural modeling with small angle X-ray scattering profiles." BMC Struct Biol 12, 17, 2012.

288. J.L. Markley, H. Akutsu, T. Asakura, M. Baldus, R. Boelens, A. Bonvin, R. Kaptein, A. Bax, I. Bezsonova, M.R. Gryk, J.C. Hoch, D.M. Korzhnev, M. Maciejewski, D. Case, W. Chazin, T. Cross, S. Dames, H. Kessler, O. Lange, T. Madl, B. Reif, M. Sattler, D. Eliezer, A. Fersht, J. Forman-Kay, L. Kay, J. Fraser, J. Gross, T. Kortemme, A. Sali, T. Fujiwara, K. Gardner, X. Luo, J. Rizo-Rey, M. Rosen, R. Gil, C. HO, G. Rule, A. Gronenborn, R. Ishima, J. Klein-Seetharaman, P. Tang, P. van der Wel, Y. Xu, S. Grzesiek, S. Hiller, J. Seelig, E. Laue, H. Mott, D. Nietlispach, I. Barsukiv, L. Lian, D. Middleton, T. Blumenschein, G. Moore, I. Campbell, J. Schnell, I. Vakonakis, A. Watts, M. Conte, J. Mason, M. Pfuhl, M. Sanderson, J. Craven, M. Williamson, C. Dominguez, G. Roberts, U. Gunther, M. Overduin, J. Werner, P. Williamson, C. Blindauer, M. Crump, P. Driscoll, T. Frenkiel, A. Golovanov, S. Matthews, J. Parkinson, D. Uhrin, M. Williams, D. Neuhaus, H. Oschkinat, A. Ramos, D. Shaw, C. Steinbeck, M. Vendruscolo, G. Vuister, K. Walters, H. Weinstein, K. Wuthrich, S. Yodoyama. "In support of the BMRB." Nat Struct Mol Biol 19, 854-860, 2012.

289. H. Fan, D. Hitchcock, R. Seidel, B. Hillerich, H. Lin, S. Almo, A. Sali, B. Shoichet, F. Raushel. "The Assignment of Pterin Deaminase Activity to an Enzyme of Unknown Function Guided by Homology Modeling and Docking." J Am Chem Soc 135, 795-803, 2013.

290. M.B. Wittwer, A.A. Zur, N. Khuri, Y. Kido, A. Kosaka, X. Zhang, K.M. Morrissey, A. Sali, Y. Huang, K.M. Giacomini. "Discovery of potent, selective multidrug and toxin extrusion Transporter 1 (MATE1, SLC47A1) inhibitors through prescription drug profiling and computational modeling." J Med Chem 56, 781-795, 2013.

291. U. Pieper, A. Schlessinger, E. Kloppmann, G.A. Chang, J.J. Chou, M. Dumont, B. Fox, P. Fromme, W. Hendrickson, M. Malkowski, D. Rees, D. Stokes, M.H.B. Stowell, M. Wiener, B. Rost, R. Stroud, R. Stevens, A. Sali. "Coordinating the impact of structural genomics on the human a-helical transmembrane proteome." Nat Struct Mol Biol 20, 135-138, 2013.

292. P. Sampathkumar, S.J. Kim, P. Upla, W. Rice, J. Phillips, B. Timney, U. Pieper, J. Bonanno, J. Fernandez-Martinez, Z. Hakhverdyan, N. Ketaren, T. Matsui, R. Weiss, D. Stokes, J.M. Sauder, S. Burley, A. Sali, M. Rout, S. Almo. "Structure, dynamics, evolution and function of a major scaffold component in the Nuclear Pore Complex." Structure 21, 560-571, 2013.

293. H. Gradisar, S. Bozic, T. Doles, D. Vengust, I. Hafner-Bratkovic, A. Mertelj, B. Webb, A. Sali, S. Klavzar, R. Jerala. "Design of a single-chain polypeptide tetrahedron assembled from coiled-coil segments." Nat Chem Biol 9, 362-366, 2013.

294. B. Pedersen, H. Kumar, A. Waight, A. Risenmay, Z. Roe-Zurz, B. Chau, A. Schlessinger, M. Bonomi, W. Harries, A. Sali, A. Johri, R. Stroud. "Crystal structure of a eukaryotic phosphate transporter." Nature 496, 533-536, 2013.

295. A. Schlessinger, N. Khuri, K. Giacomini, A. Sali. "Molecular modeling and ligand docking for Solute Carrier (SLC) transporters." Curr Top Med Chem 13, 843-856, 2013.

296. T. van Dam, M. Townsend, M. Turk, A. Schlessinger, A. Sali, M. Field, M. Huynen. "Evolution of modular intraflagellar transport from a coatomer-like progenitor." Proc Natl Acad Sci USA 110, 6943-6948, 2013.

297. A. Waight, B. Pedersen, A. Schlessinger, M. Bonomi, B. Chau, Z. Roe-Zurz, A. Risenmay, A. Sali, R. Stroud. "Structural basis for alternating access of a Eukaryotic Calcium/Proton exchanger." Nature 499, 107-110, 2013.

298. M. Guttman, P. Weinkam, A. Sali, K. Lee. "All-atom ensemble modeling to analyze small angle X-ray scattering of glycosylated proteins." Structure 21, 321-331, 2013.

299. P. Weinkam, Y.C. Chen, J. Pons, A. Sali. "Impact of mutations on the allosteric conformational equilibrium." J Mol Biol 425, 647-661, 2013.

300. A. Ward, A. Sali, I. Wilson. "Integrative structural biology." Science 339, 913-915, 2013.

301. E. Geier, A. Schlessinger, H. Fan, J. Gable, J. Irwin, A. Sali, K. Giacomini. "Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1." Proc Natl Acad Sci USA 110, 5480-5485, 2013.

304. D. Schneidman-Duhovny, M. Hammel, J. Tainer, A. Sali. "Accurate SAXS profile computation and its assessment by contrast variation experiments." Biophys J 105, 962-974, 2013.

305. D. Hitchcock, H. Fan, J. Kim, M. Vetting, B. Hillerich, R. Seidel, S. Almo, B. Shoichet, A. Sali, F. Raushel. "Structure-guided Discovery of New Deaminase Enzymes." J Am Chem Soc 135, 13927-13933, 2013.

310. M. Kostic, C. Lima, A. Sali. "Celebrating 20 Years of Structural Biology." Structure 21, 1477-1478, 2013.

312. C. Ryan, P. Cimermancic, Z. Szpiechy, A. Sali, R. Hernandez, N. Krogan. "High-resolution network biology: connecting sequence with function." Nat Rev Genet 14, 865-879, 2013.

313. K. Berlin, C.A. Castaneda, D. Schneidman-Duhovny, A. Sali, A. Nava-Tudela, D. Fushman. "Recovering a representative conformational ensemble from underdetermined macromolecular structural data." J Am Chem Soc 135, 16595-16609, 2013.

314. B. Webb, N. Eswar, H. Fan, N. Khuri, U. Pieper, G.Q. Dong, A. Sali. "Comparative Modeling of Drug Target Proteins." In: Chemistry, Molecular Sciences and Chemical Engineering. Ed: J. Reedijk, Elsevier, Waltham, MA, 2014.

316. M. Bonomi, E.G. Muller, R. Pellarin, S.J. Kim, D. Russel, R. Ramsden, B.A. Sundin, T.A. Davis, A. Sali. "Determining protein complex structures based on a Bayesian model of in vivo FRET data." Mol Cell Proteomics 13, 2812-2823, 2014.

319. B. Webb, K. Lasker, J. Velazquez-Muriel, D. Schneidman-Duhovny, R. Pellarin, M. Bonomi, C. Greenberg, B. Raveh, E. Tjioe, D. Russel, A. Sali. "Modeling of proteins and their assemblies with the Integrative Modeling Platform." In: Methods Mol Biol. Ed: Y. Chen, 1091, pp. 277-295, Humana Press, London, UK, 2014.

320. Y. Spill, S.J. Kim, D. Schneidman-Duhovny, D. Russel, B. Webb, A. Sali, M. Nilges. "SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes." J Synchrotron Radiat 21, 203-208, 2014.

322. R. Algret, J. Fernandez-Martinez, Y. Shi, S.J. Kim, R. Pellarin, P. Cimermancic, E. Cochet, A. Sali, B. Chait, M. Rout, S. Dokudovskaya. "Molecular Architecture and Function of the SEA Complex  - a Modulator of the TORC1 Pathway." Mol Cell Proteomics 13, 2855-2870, 2014.

324. X. Zeng-Elmore, X. Gao, R. Pellarin, D. Schneidman-Duhovny, X. Zhang, K. Kozacka, Y. Tang, A. Sali, R. Chalkley, R. Cote, F. Chu. "Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling." J Mol Biol 426, 3713-3728, 2014.

325. J. Erzberger, F. Stengel, R. Pellarin, S. Zhang, T. Schaefer, C. Aylett, P. Cimermancic, D. Boehringer, A. Sali, R. Aebersold, N. Ban. "Molecular architecture of the 40S•eIF1•eIF3 translation initiation complex." Cell 158, 1125-1135, 2014.

327. P. Cimermancic, M.H. Medema, J. Claesen, K. Kurita, L. Wieland Brown, K. Mavrommatis, A. Pati, P.A. Godfrey, M. Koehrsen, J. Clardy, B.W. Birren, E. Takano, A. Sali, R.G. Linington, M. Fischbach. "Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters." Cell 158, 412-421, 2014.

328. M.H. Medema, P. Cimermancic, A. Sali, E. Takano, M. Fischbach. "A systematic computational analysis of biosynthetic gene cluster evolution: Lessons for engineering biosynthesis." PLoS Comput Biol 10, e1004016, 2014.

329. S.J. Kim, J. Fernandez-Martinez, P. Sampathkumar, A. Martel, T. Matsui, H. Tsuruta, T. Weiss, A. Markina-Inarrairaegui, J. Bonanno, M. Sauder, S. Burley, B.T. Chait, S. Almo, M. Rout, A. Sali. "Integrative Structure-Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex." Mol Cell Proteomics 13, 2911-2926, 2014.

330. Y. Shi, J. Fernandez-Martinez, E. Tjioe, R. Pellarin, S.J. Kim, R. Williams, D. Schneidman, A. Sali, M. Rout, B. Chait. "Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex." Mol Cell Proteomics 13, 2927-2943, 2014.

331. B. Webb, A. Sali. "Comparative Protein Structure Modeling Using Modeller." In: Curr Protoc Bioinformatics, 47, pp. 5.6.1-5.6.32, John Wiley and Sons, 2014.

333. A. Politis, C. Schmidt, E. Tjioe, A. Sandercock, K. Lasker, Y. Gordiyenko, D. Russel, A. Sali, C. Robinson. "Topological models of heteromeric protein assemblies from mass spectrometry: Application to the yeast eIF3:eIF5 complex." Chem Biol 22, 117-128, 2015.

334. J. Kollman, C. Greenberg, S. Li, M. Moritz, A. Zelter, K. Fong, J. Fernandez, A. Sali, J. Kilmartin, T. Davis, D. Agard. "Ring closure activates yeast γTuRC for species-specific microtubule nucleation." Nat Struct Mol Biol 22, 132-137, 2015.

335. J. Johnson, S. Santos, U. Pieper, A. Sali, N. Krogan, P. Beltrao. "Prediction of functionally important phospho-regulatory events in Xenopus laevis oocytes." PLOS Comp Bio 11, e1004362, 2015.

336. A. Sali, H. Berman, T. Schwede, J. Trewhella, G. Kleywegt, S. Burley, J. Markley, H. Nakamura, P. Adams, A. Bonvin, W. Chiu, M. Dal Peraro, F. Di Maio, T. Ferrin, K. Grunewald, A. Gutmanas, R. Henderson, G. Hummer, K. Iwasaki, G. Johnson, C. Lawson, J. Meiler, M. Marti-Renom, G. Montelione, M. Nilges, R. Nussinov, A. Patwardhan, J. Rappsilber, R. Read, H. Saibil, G. Schroder, C. Schwieters, C. Seidel, D. Svergun, M. Topf, E. Ulrich, S. Velanker, J. Westbrook. "Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop." Structure 23, 1156-67, 2015.

338. Y. Shi, R. Pellarin, P. Fridy, J. Fernandez-Martinez, M. Thompson, Y. Li, Q.J. Wang, A. Sali, M. Rout, B. Chait. "A strategy for dissecting the architectures of native macromolecular assemblies." Nat Methods 12, 1135-8, 2015.

339. J. Luo, P. Cimermancic, S. Viswanath, C. Ebmeier, B. Kim, M. Dehecq, V. Raman, C. Greenberg, R. Pellarin, A. Sali, D. Taatjes, S. Hahn, J. Ranish. "Architecture of the human and yeast general transcription and DNA repair factor TFIIH." Mol Cell 59, 794-806, 2015.

340. P. Robinson, M. Trnka, R. Pellarin, C. Greenberg, D. Bushnell, R. Davis, A. Burlingame, A. Sali, R. Kornberg. "Molecular architecture of the yeast Mediator complex." eLife 4, e08719, 2015.

341. R. Reid, M. Sgobba, B. Raveh, G. Rastelli, A. Sali, D. Santi. "Analytical and simulation-based models for drug release and gel-degradation in a Tetra-PEG hydrogel drug-delivery system." Macromolecules 48, 7359-7369, 2015.

342. C. Smith, K. Lin, A. Stecula, A. Sali, N. Shah. "FLT3 D835 mutations confer differential resistance to type II FLT3 inhibitors." Leukemia 29, 2390-2, 2015.

343. A.R. Choudhury, E. Sikorska, J. van den Boom, P. Bayer, L. Popenda, K. Szutkowski, S. Jurga, M. Bonomi, A. Sali, I. Zhukov, S. Passamonti, M. Novič. "Structural model of the Bilitranslocase transmembrane domain supported by NMR and FRET data." PloS One 10, e0135455, 2015.

344. T. Rettenmaier, H. Fan, J. Karpiak, A. Doak, A. Sali, B. Shoichet, J. Wells. "Small-molecule allosteric modulators of the protein kinase PDK1 from structure-based docking." J Med Chem 58, 8285-91, 2015.

345. J. LoPiccolo, S.J. Kim, Y. Shi, B. Wu, H. Wu, B.T. Chait, R.H. Singer, A. Sali, M. Brenowitz, A.R. Bresnick, J.M. Backer. "Assembly and Molecular Architecture of the Phosphoinositide 3-Kinase p85α Homodimer." J Biol Chem 290, 30390-405, 2015.

346. P. Cimermancic, P. Weinkam, T.J. Rettenmaier, L. Bichmann, D.A. Keedy, R.A. Woldeyes, D. Schneidman-Duhovny, O.N. Demerdash, J.C. Mitchell, J.A. Wells, J.S. Fraser, A. Sali. "CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites." J Mol Biol 428, 709-19, 2016.

347. E. Lasater, E. Massi, A. Stecula, J. Politi, S. Tan, C. Smith, M. Gunthorpe, J. Holmes, F. Chehab, A. Sali, N. Shah. "Novel TKI-resistant BCR-ABL1 Gatekeeper Residue Mutations Retain in vitro Sensitivity to Axitinib." Leukemia 30, 1405-9, 2016.

348. D. Schneidman-Duhovny, N. Khuri, G.Q. Dong, M.B. Winter, E. Shifrut, N. Friedman, C.S. Craik, K.P. Pratt, P. Paz, F. Aswad, A. Sali. "Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition." submitted.

349. J. Sprowl, S.S. Ong, A. Gibson, S. Hu, G. Du, W. Lin, L. Li, S. Bharill, R. Ness, A. Stecula, S. Offer, R. Diasio, A. Nies, M. Schwab, G. Cavaletti, E. Schlatter, G. Ciarimboli, J. Schellens, E. Isacoff, A. Sali, T. Chen, S. Baker, A. Sparreboom, N. Pabla. "A phosphotyrosine switch regulates organic cation transporters." Nat Commun 7, 10880, 2016.

350. M.F. Lensink, S. Velankar, A. Kryshtafovych, S. Huang, D. Schneidman-Duhovny, A. Sali, J. Segura, N. Fernandez-Fuentes, S. Viswanath, R. Elber, S. Grudinin, P. Popov, E. Neveu, H. Lee, M. Baek, S. Park, L. Heo, G.R. Lee, C. Seok, S. Qin, H. Zhou, D.W. Ritchie, B. Maigret, M. Devignes, A. Ghoorah, M. Torchala, R.A.G. Chaleil, P.A. Bates, E. Ben-Zeev, M. Eisenstein, S.S. Negi, Z. Weng, T. Vreven, B.G. Pierce, T.M. Borrman, J. Yu, F. Ochsenbein, R. Guerois, A. Vangone, J.P.G.L.M. Rodrigues, G. van Zundert, M. Nellen, L. Xue, E. Karaca, A.S.J. Melquiond, K. Visscher, P.L. Kastritis, A.M.J.J. Bonvin, X. Xu, L. Qiu, C. Yan, J. Li, Z. Ma, J. Cheng, X. Zou, Y. Shen, L.X. Peterson, H. Kim, A. Roy, X. Han, J. Esquivel-Rodriguez, D. Kihara, X. Yu, N.J. Bruce, J.C. Fuller, R.C. Wade, I. Anishchenko, P.J. Kundrotas, I.A. Vakser, K. Imai, K. Yamada, T. Oda, T. Nakamura, K. Tomii, C. Pallara, M. Romero-Durana, B. Jiménez-García, I.H. Moal, J. Férnandez-Recio, J.Y. Joung, J.Y. Kim, K. Joo, J. Lee, D. Kozakov, S. Vajda, S. Mottarella, D.R. Hall, D. Beglov, A. Mamonov, B. Xia, T. Bohnuud, C.A. Del Carpio, E. Ichiishi, N. Marze, D. Kuroda, S.S.R. Burman, J.J. Gray, E. Chermak, L. Cavallo, R. Oliva, A. Tovchigrechko, S.J. Wodak. "Prediction of homo- and hetero-protein complexes by ab-initio and template-based docking: a CASP-CAPRI experiment." Proteins 84 Suppl 1, 323-48, 2016.

351. B. Raveh, J.M. Karp, S. Sparks, K. Dutta, M.P. Rout, A. Sali, D. Cowburn. "Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex." Proc Natl Acad Sci USA 113, E2489-97, 2016.

352. D. Schneidman, M. Hammel, J. Tainer, A. Sali. "FoXS, FoXSDock, and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles." Nucleic Acids Res 44, W424-9, 2016.

353. Z.A. Chen, R. Pellarin, L. Fischer, A. Sali, M. Nilges, P.N. Barlow, J. Rappsilber. "Structure of complement C3(H2O) revealed by quantitative cross-linking/mass spectrometry and modelling." Mol Cell Proteomics 15, 2730-2743, 2016.

354. A. Jahangiri, S.W. Han, M.K. Sidorov, W. Chen, J. Rick, D. Schneidman-Duhovny, S. Mascharak, M. De Lay, J.R. Wagner, B. Imber, P.M. Flanigan, A. Chandra, R. Kuang, B.A. Castro, K. Lu, G. Bergers, A. Sali, W.A. Weiss, M.K. Aghi. "A cross-activating c-Met/β1 integrin complex drives therapeutic resistance." PNAS, in press.

355. J.C. Watts, K. Giles, D.J. Saltzberg, B.N. Dugger, S. Patel, A. Oehler, S. Bhardwaj, A. Sali, S.B. Prusiner. "Guinea Pig Prion Protein Supports Rapid Propagation of Bovine Spongiform Encephalopathy and Variant Creutzfeldt-Jakob Disease Prions." J Virol 90, 9558-9569, 2016.

356. U. Schulze-Gahmen, I. Echeverria, G. Stjepanovic, Y. Bai, H. Lu, D. Schneidman-Duhovny, J.A. Doudna, Q. Zhou, A. Sali, J.H. Hurley. "Insights into HIV-1 proviral transcription from the structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex." eLife 5, e15910, 2016.

357. B.L. Timney, B. Raveh, R. Mironska, J.M. Trivedi, S.J. Kim, D. Russel, S.R. Wente, A. Sali, M.P. Rout. "Simple rules for passive diffusion through the nuclear pore complex." J Cell Biol 215, 57-76, 2016.

358. D.T. Barkan, X. Cheng, H. Celino, T. Tran, A. Bhandari, C.S. Craik, A. Sali, M.L. Smythe. "Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23." BMC Bioinformatics 17, 481, 2016.

359. D.J. Saltzberg, H.B. Broughton, R. Pellarin, M.J. Chalmers, A. Espada, J.A. Dodge, B.D. Pascal, P.R. Griffin, C. Humblet, A. Sali. "A Residue Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions." J Phys Chem B 121, 3493-3501, 2016.

360. J. Fernandez-Martinez, S.J. Kim, Y. Shi, P. Upla, R. Pellarin, M. Gagnon, I.E. Chemmama, J. Wang, I. Nudelman, W. Zhang, R. Williams, W.J. Rice, D.L. Stokes, D. Zenklusen, B.T. Chait, A. Sali, M.P. Rout. "Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform." Cell 167, 1215-1228, 2016.

361. C.H. Greenberg, J. Kollman, A. Zelter, R. Johnson, M.J. MacCoss, T.N. Davis, D.A. Agard, A. Sali. "Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure." J Struct Biol 194, 303-10, 2016.

362. X. Wang, P. Cimermancic, C. Yu, E. Sakata, X. Guo, C. Greenberg, A. Schweitzer, A.S. Huszagh, Y. Yang, E.J. Novitsky, A. Leitner, P. Nanni, A. Kahraman, J. Dixon, S.D. Rychnovsky, R. Aebersold, W. Baumeister, A. Sali, L. Huang. "Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome." Mol Cell Proteomics, mcp.M116.065326 [Epub ahead of print], 2017.

363. S. Calhoun, M. Korczynska, D.J. Wichelecki, B. San Francisco, S. Zhao, D.A. Rodionov, M.W. Vetting, N.F. Al-Obaidi, H. Lin, M.J. O’Meara, D.A. Scott, J.H. Morris, D. Russel, S.C. Almo, A.L. Osterman, J.A. Gerlt, M.P. Jacobson, B.K. Shoichet, A. Sali. "Integrative mapping of enzymatic pathways." submitted.

364. P. Fromme, A. Sali. "Editorial overview: Biophysical and molecular biological methods." Curr Opin Struct Biol 40, ix-xi, 2016.

365. B. Webb, A. Sali. "Comparative Protein Structure Modeling Using MODELLER." In: Curr Protoc Protein Sci, 86, pp. 2.9.1-2.9.37, John Wiley and Sons, 2016.

366. B. Webb, A. Sali. "Comparative Protein Structure Modeling Using MODELLER." In: Curr Protoc Bioinformatics, 54, pp. 5.6.1-5.6.37, John Wiley and Sons, 2016.

367. N. Khuri, A. Zur, M. Wittwer, L. Lin, S.W. Yee, A. Sali, K. Giacomini. "Computational Discovery And Experimental Validation of Inhibitors of the Human Intestinal Transporter, OATP2B1." J Chem Inf Model [Epub ahead of print].

368. A. Chen, M. Vieth, D. Timm, C. Humblet, D. Schneidman-Duhovny, I.E. Chemmama, A. Sali, J. Lu, L. Liu. "Reconstruction of 3D structures of MET Antibodies from Electron Microscopy 2D Class Averages." PloS One 12, e0175758, 2017.

369. E.C. Chen, N. Khuri, X. Liang, A. Stecula, H. Chien, S.W. Yee, Y. Huang, A. Sali, K.M. Giacomini. "Discovery of competitive and non-competitive ligands of the organic cation transporter 1 (OCT1; SLC22A1)." J Med Chem, in press.

370. B. Webb, A. Sali. "Protein structure modeling with MODELLER." In: Methods in Molecular Biology, in press.

371. P. Upla, S.J. Kim, P. Sampathkumar, K. Dutta, S.M. Cahill, I.E. Chemmama, R. Williams, J.B. Bonanno, W.J. Rice, D.L. Stokes, D. Cowburn, S.C. Almo, A. Sali, M.P. Rout, J. Fernandez-Martinez. "Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex." Structure 25, 434-445, 2017.

372. P.T. Manna, S. Obado, C. Boehm, C. Gadelha, G. van Miero, A. Sali, B. Chait, M. Rout, M.C. Field. "Lineage-specific proteins essential for endocytosis in trypanosomes." J Cell Sci 130, 1379-1392, 2017.

373. A. Stecula, A. Schlessinger, K. Giacomini, A. Sali. "Human concentrative nucleoside transporter 3 (hCNT3, SLC28A3) forms a cyclic homo-trimer." Biochemistry, in press.

374. C.Y. Zhou, C.I. Stoddard, J.B. Johnston, M.J. Trnka, I. Echeverria, E. Palovcak, A. Sali, A.L. Burlingame, Y. Cheng, G.J. Narlikar. "Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones." Cell Rep 19, 2033-2044, 2017.

375. S.K. Burley, G. Kurisu, J.L. Markley, H. Nakamura, S. Velankar, H.M. Berman, A. Sali, T. Schwede, J. Trewhella. "PDB-Dev: A Prototype System for Depositing Integrative/Hybrid Structural Models." Structure 25, 1317-1318, 2017.

376. J. Trewhella, A.P Duff, D. Durand, F. Gabel, J.M. Guss, W.A. Hendrickson, G.L. Hura, D.A. Jacques, N.M. Kriby, A.H. Kwan, J. Perez, L. Pollack, T.M. Ryan, A. Sali, D. Schneidman-Duhovny, T. Schwede, D.I. Svergun, M. Sugiyama, J.A. Tainer, P. Vachette, J. Westbrook, A.E. Whitten. "2017 Publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update." Acta Cryst D D73, 710-728, 2017.

377. S. Viswanath, M. Bonomi, S.J. Kim, V.A. Klenchin, K.C. Taylor, K.C. Yabut, N.T. Umbreit, H.A. Van Epps, J. Meehl, M.H. Jones, D. Russel, J.A. Velazquez-Muriel, M. Winey, I. Rayment, T.N. Davis, A. Sali, E.G. Muller. "The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling." Mol Biol Cell, in press.

378. S. Viswanath, I. Chemmama, P. Cimermancic, A. Sali. "Validating Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures." submitted.

379. T. Yoshizawa, R. Ali, H.Y.J. Fung, K.A. Burke, Y. Lin, S.J. Kim, J. Jiou, M. Soniat, R. Oldenbourg, A. Sali, N.L. Fawzi, M.K. Rosen, Y.M. Chook. "Karyopherin-β2 inhibits phase separation of FUS through binding to multiple sites." submitted.

380. B. Webb, S. Viswanath, M. Bonomi, R. Pellarin, C.H. Greenberg, D. Saltzberg, A. Sali. "Integrative structure modeling with IMP." submitted.

381. X. Wang, I.E. Chemmama, C. Yu, A. Huszagh, Y. Xu, R. Viner, S.A. Block, P. Cimermancic, S. Rychnovsky, Y. Ye, A. Sali, L. Huang. "Human 26S Proteasome Is Regulated upon Oxidative Stress via Interaction with Ecm29." J Biol Chem, in press.

382. M.B. Winter, F. La Greca, P. Cimermancic, T.J. Buchholz, J.L. Anderl, S. Arastu-Kapur, A. Sali, A.J. O’Donoghue, C.S. Craik. "Distinguishing the Human Immuno- and Constitutive Proteasomes with Global Substrate Specificity Profiling." submitted.