Scoring protein-protein docked structures based on the balance and tightness of binding

Journal of Computer-Aided Molecular Design

Volumn 18, Issue 4, 2004, Pages 251-260

  Yu, Y H ^a   Lu, B Z ^a,b   Han, J G ^b   Zhang, P F ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

Balance and tightness of binding; Protein protein docking; Scoring function

Indexed keywords

ANTIBODIES; BINDING ENERGY;

ANTIBODY-ANTIGEN; BALANCE AND TIGHTNESS OF BINDING; ENZYME INHIBITORS; INTERACTION POTENTIALS; PROTEIN-PROTEIN DOCKING; PROTEIN-PROTEIN INTERACTIONS; SCORING FUNCTIONS; SECOND ORDERS; SPATIAL DERIVATIVES; STRUCTURE-BASED;

FREE ENERGY;

LIGAND; PROTEIN DERIVATIVE;

ANTIGEN ANTIBODY COMPLEX; ARTICLE; ATOM; CONTROLLED STUDY; CORRELATION ANALYSIS; ENERGY; ENZYME INHIBITOR COMPLEX; FILTRATION; FORCE; GEOMETRY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING; PROTEIN TRANSPORT;

EID: 8144231288     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:JCAM.0000046753.03033.3a     Document Type: Article

References (29)

1. Sternberg, M.J.E., Gabb, H.A. and Jackson, R.M., Curr. Opin. Struct. Biol., 8 (1998) 250.
2. Smith, G.R. and Sternberg, M.E.J., Curr. Opin. Struct. Biol., 12 (2002) 28.
3. Halperin, I., Ma, B., Wolfson, H. and Nussinov, R., Proteins, 47 (2002) 409.
4. Kuntz, I., Blaney, J., Oatley, S., Langridge, R. and Ferrin, T.A., J. Mol. Biol., 161 (1982) 269.
5. Connoly, M., Biopolymers, 25 (1986) 1229.
6. Norel, R., Petrtrey, D., Wolfson, H. and Nussinov, R., Proteins, 35 (1999) 403.
7. Gardina, E.J., Willett, P. and Artimiuk, P.J., Proteins, 44 (2001) 44.
8. Palma, P.N., Krippahl, L., Wampler, J.E. and Moura, J.J.G., Proteins, 39 (2000) 178.
9. Jackson, R.M., Gabb, H.A. and Sternberg, M.J.E., J. Mol. Biol., 276 (1998) 265.
10. Jackson, R.M. and Sternberg, M.J.E., J. Mol. Biol., 250 (1995) 258.
11. Weng, Z., Vajda, S. and DeLisi, C., Protein Sci., 5 (1996) 614.
12. Wallquist, A. and Covell, D.G., Proteins, 35 (1996) 403.
13. Zhang, C., Vasmatzis, G., Cornette, J.L. and DeLisi., C., J. Mol. Biol., 267 (1997) 707.
14. Camacho, C.J., Gatchell, D.W., Kimura, S.R. and Vajda, S., Proteins, 40 (2000) 525.
15. Pearlman, D.A. and Charifson, P.S., J. Med. Chem., 44 (2001) 3417.
16. Gatchell, D.W., Dennis, S. and Vajda, S., Proteins, 41 (2000) 518.
17. Vajda, S., Sippl, M. and Novotny, J., Curr. Opin. Struct. Biol., 7 (1997) 222.
18. Srinivasan, J., Cheatham III, T.E., Cieplak, P., Kollman, P.A. and Case, D.A., J. Am. Chem. Soc., 120 (1998) 9401.
19. Wang, W. and Koffman, P.A., J. Mol. Biol., 303 (2000) 567.
20. Straatsma, T.P. and McCammon, J.A., Ann. Rev. Phys. Chem., 43 (1992) 407.
21. Li, L., Chen, R. and Weng, Z.P., Proteins, 53 (2003) 693.
22. Onuchic, J.N., Wolynes, P.G., Luthey-Schulten, Z. and Socci, N.D., Proc. Natl. Acad. Sci. USA, 92 (1995) 3626.
23. Tsai, C.J., Kumar, S., Ma, B. and Nussinov, R., Protein Sci.,8 (1999) 1181.
24. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S. and Karplus, M., J. Comput. Chem., 4 (1983) 187.
25. Wodak, S.J. and Janin, J., J. Mol. Biol., 124 (1978) 323.
26. Cherfils, J., Duquerroy, S. and Janin, J., Proteins, 11 (1991) 271.
27. Li, C.H., Ma, X.H., Chen, W.Z. and Wang, C.X, Protein Eng., 16 (2003) 265.
28. Camacho, C.J., Weng, Z., Vajda, S. and DeLisi, C., Biophys. J., 76 (1999) 1166.
29. Hu, Z., Ma, M., Wolfson, H. and Nussinov, R., Proteins, 39 (2000) 331.