Optimizing energy functions for protein-protein interface design

Journal of Computational Chemistry

Volumn 32, Issue 1, 2011, Pages 23-32

  Sharabi, Oz ^a   Yanover, Chen ^b   Dekel, Ayelet ^a   Shifman, Julia M ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^b Fred Hutchinson Cancer Research Center   (United States)

Author keywords

computational protein design; conditional random fields; energy functions; heterodimers; optimization; protein protein interactions

Indexed keywords

COMPUTATIONAL PROTEIN DESIGN; CONDITIONAL RANDOM FIELD; ENERGY FUNCTIONS; HETERODIMERS; PROTEIN-PROTEIN INTERACTIONS;

AMINO ACIDS; BINDING ENERGY; BIOCHEMICAL ENGINEERING; COMPLEXATION; ELECTROSTATICS; HYDROGEN BONDS; OPTIMIZATION; VAN DER WAALS FORCES;

PROTEINS;

PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; HYDROGEN BOND; THERMODYNAMICS;

COMPUTER SIMULATION; HYDROGEN BONDING; MODELS, MOLECULAR; PROTEINS; THERMODYNAMICS;

EID: 78649573900     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21594     Document Type: Article

References (41)

1. Chevalier, B. S.;Kortemme, T.;Chadsey, M. S.;Baker, D.;Monnat, R. J.;Stoddard, B. L., Mol Cell 2002, 10, 895.
2. Rothlisberger, D.;Khersonsky, O.;Wollacott, A. M.;Jiang, L.;DeChancie, J.;Betker, J.;Gallaher, J. L.;Althoff, E. A.;Zanghellini, A.;Dym, O.;Albeck, S.;Houk, K. N.;Tawfik, D. S.;Baker, D., Nature 2008, 453, 190.
3. Jiang, L.;Althoff, E. A.;Clemente, F. R.;Doyle, L.;Rothlisberger, D.;Zanghellini, A.;Gallaher, J. L.;Betker, J. L.;Tanaka, F.;Barbas, C. F., III;Hilvert, D.;Houk, K. N.;Stoddard, B. L.;Baker, D., Science 2008, 319, 1387.
4. Looger, L. L.;Dwyer, M. A.;Smith, J. J.;Hellinga, H. W., Nature 2003, 423, 185.
5. Benson, D. E.;Conrad, D. W.;de Lorimier, R. M.;Trammell, S. A.;Hellinga, H. W., Science 2001, 293, 1641.
6. Steed, P. M.;Tansey, M. G.;Zalevsky, J.;Zhukovsky, E. A.;Desjarlais, J. R.;Szymkowski, D. E.;Abbott, C.;Carmichael, D.;Chan, C.;Cherry, L.;Cheung, P.;Chirino, A. J.;Chung, H. H.;Doberstein, S. K.;Eivazi, A.;Filikov, A. V.;Gao, S. X.;Hubert, R. S.;Hwang, M.;Hyun, L.;Kashi, S.;Kim, A.;Kim, E.;Kung, J.;Martinez, S. P.;Muchhal, U. S.;Nguyen, D. H.;O'Brien, C.;O'Keefe, D.;Singer, K.;Vafa, O.;Vielmetter, J.;Yoder, S. C.;Dahiyat, B. I., Science 2003, 301, 1895.
7. Shifman, J. M.;Mayo, S. L., J Mol Biol 2002, 323, 417.
8. Shifman, J. M.;Mayo, S. L., Proc Natl Acad Sci U S A 2003, 100, 13274.
9. Grigoryan, G.;Reinke, A. W.;Keating, A. E., Nature 2009, 458, 859.
10. Yosef, E.;Politi, R.;Choi, M. H.;Shifman, J. M., J Mol Biol 2009, 385, 1470.
11. Yin, H.;Slusky, J. S.;Berger, B. W.;Walters, R. S.;Vilaire, G.;Litvinov, R. I.;Lear, J. D.;Caputo, G. A.;Bennett, J. S.;DeGrado, W. F., Science 2007, 315, 1817.
12. Joachimiak, L. A.;Kortemme, T.;Stoddard, B. L.;Baker, D., J Mol Biol 2006, 361, 195.
13. Guerois, R.;Nielsen, J. E.;Serrano, L., J Mol Biol 2002, 320, 369.
14. Dahiyat, B. I.;Gordon, D. B.;Mayo, S. L., Protein Sci 1997, 6, 1333.
15. Kim, D. E.;Chivian, D.;Baker, D., Nucleic Acids Research 2004, 32, W526-W531.
16. Pokala, N.;Handel, T. M., J Mol Biol 2005, 347, 203-227.
17. Gordon, D. B.;Marshall, S. A.;Mayo, S. L., Curr Opin Struct Biol 1999, 9, 509.
18. Dahiyat, B. I.;Mayo, S. L., Protein Sci 1996, 5, 895.
19. Dahiyat, B. I.;Mayo, S. L., Proc Natl Acad Sci U S A 1997, 94, 10172.
20. Kuhlman, B.;Baker, D., Proc Natl Acad Sci U S A 2000, 97, 10383.
21. Raha, K.;Wollacott, A. M.;Italia, M. J.;Desjarlais, J. R., Protein Sci 2000, 9, 1106.
22. Dahiyat, B. I.;Gordon, D. B.;Mayo, S. L., Protein Sci 1997, 6, 1333.
23. Malakauskas, S. M.;Mayo, S. L., Nat Struct Biol 1998, 5, 470.
24. Hu, X. Z.;Wang, H. C.;Ke, H. M.;Kuhlman, B., Structure 2008, 16, 1799.
25. Benedix, A.;Becker, C. M.;de Groot, B. L.;Caflisch, A.;Bockmann, R. A., Nat Meth 2009, 6, 3.
26. Xu, D.;Lin, S. L.;Nussinov, R., J Mol Biol 1997, 265, 68.
27. Dahiyat, B. I.;Mayo, S. L., Protein Sci 1996, 5, 895.
28. Schreiber, G.;Fersht, A. R., J Mol Biol 1995, 248, 478.
29. Sutton, C.;McCallum, A., In Introduction to Statistical Relational Learning;, Getoor, L., Taskar, B., Eds.; MIT Press: Cambridge, 2007.
30. Cohen, M.;Reichmann, D.;Neuvirth, H.;Schreiber, G., Proteins: Struct Funct Bioinfor 2008, 72, 741.
31. Dunbrack, R. L.;Karplus, M., J Mol Biol 1993, 230, 543.
32. Yanover, C.;Schueler-Furman, O.;Weiss, Y., J Comput Biol 2008, 15, 899.
33. Yanover, C.;Weiss, Y., In Advances in Neural Information Processing Systems;, Becker, S.;Thrun, S.;Obermayer, K., Eds.; MIT Press: Cambridge, 2003; pp. 1457-1464.
34. Pearl, J., Probabilistic Reasoning in Intelligent Systems: Networks of Plausible Inference; Morgan Kaufmann: San Mateo, CA, 1988.
35. Desmet, J.;De Maeyer, M.;Hazes, B.;Lasters, I., Nature 1992, 356, 539.
36. Allen, B. D.;Mayo, S. L., J Comput Chem 2006, 27, 1071.
37. Sammond, D. W.;Eletr, Z. M.;Purbeck, C.;Kimple, R. J.;Siderovski, D. P.;Kuhlman, B., J Mol Biol 2007, 371, 1392.
38. Dantas, G.;Corrent, C.;Reichow, S. L.;Havranek, J. J.;Eletr, Z. M.;Isern, N. G.;Kuhlman, B.;Varani, G.;Merritt, E. A.;Baker, D., J Mol Biol 2007, 366, 1209.
39. Grigoryan, G.;Ochoa, A.;Keating, A. E., Proteins 2007, 68, 863.
40. Shifman, J. M.;Choi, M. H.;Mihalas, S.;Mayo, S. L.;Kennedy, M. B., Proc Nat Acad Sci U S A 2006, 103, 13968.
41. Andrusier, N.;Nussinov, R.;Wolfson, H. J., Proteins: Struct Funct Bioinfor 2007, 69, 139.