A fast empirical approach to binding free energy calculations based on protein interface information

Protein Engineering

Volumn 15, Issue 8, 2002, Pages 677-681

  Ma, Xiao Hui ^a   Wang, Cun Xin ^a   Li, Chun Hua ^a   Chen, Wei Zu ^a  

^a BEIJING UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Docking; Entropy; Intermolecular interactions; Protein association

Indexed keywords

ARTICLE; BINDING AFFINITY; CALCULATION; COMPLEX FORMATION; ENERGY; ENTROPY; MATHEMATICAL ANALYSIS; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

EID: 0036699164     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/15.8.677     Document Type: Article

References (33)

1. Berendsen, H.J.C., van der Spoel, D. and van Drunen, R. (1995) Comput. Phys. Commun., 91, 43-56.
2. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B, Meyer, E.F., Brice, MD., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977) J. Mol. Biol., 112, 535-542.
3. Camacho, C.J. and Vajda, S. (2002) Curr. Opin. Struct. Biol., 12, 36-40.
4. Camacho, C.J., Weng, Z., Vajda, S. and DeLisi, C. (1999) Biophys J., 76, 1166-1178.
5. Cherfils, J. and Janin, J. (1993) Curr. Opin. Struct. Biol., 3, 265-269.
6. Cherfils, J., Duquerroy, S. and Janin, J. (1991) Proteins: Struct. Funct. Genet., 11, 271-280.
7. Cherfils, J., Bizebard, T., Knossow, M. and Janin, J. (1994) Proteins: Struct. Funct. Genet., 18, 8-18.
8. Di Nola, A., Berendsen, H.J.C. and Edholm, O. (1984) Macromolecules, 17, 2044-2050.
9. Goodsell, D.S. and Olson, A.J. (1990) Proteins: Struct. Funct. Genet., 8, 195-202.
10. Jackson, R.M. and Sternberg, M.J. (1995) J. Mol. Biol., 250, 258-275.
11. Karplus, M. and Kushick J.N. (1981) Macromolecules, 14, 325-332.
12. Karplus, M. and Petsko, G.A. (1990) Nature, 347, 631-639.
13. King, B.L., Vajda, S. and DeLisi, C. (1996) FEBS Lett., 384, 87-91.
14. Lee, B. and Richards F.M. (1971) J. Mol. Biol., 55, 379-400.
15. Lin, S.L., Nussinov, R., Fischer, D. and Wolfson, H.J. (1994) Proteins: Struct. Funct. Genet., 18, 94-101.
16. Mezei, M. and Beveridge, D.L. (1986) Ann. N. Y. Acad. Sci., 482, 1-23.
17. Miyamoto, S. and Kollman, P.A. (1993) Proteins: Struct. Funct. Genet., 16, 226-245.
18. Nauchitel, V., Villaverde, M.C. and Sussman, F. (1995) Protein Sci., 4, 1356-1364.
19. Norel, R., Sheinerman, F., Petrey, D. and Honig, B. (2001) Protein Sci., 10, 2147-2161.
20. Novotny, J., Bruccoleri, R.E. and Saul, F.A. (1989) Biochemistry, 28, 4735-4749.
21. Pickett, S.D. and Sternberg, M.J.E. (1993) J. Mol. Biol., 231, 825-839.
22. Reynolds, C.A., King, P.M. and Richards, W.G. (1992) Mol. Phys., 76, 251-275.
23. Sezerman, U., Vajda, S., Cornette, J., DeLisi, C. (1993) Protein Sci., 2, 1827-1843.
24. Smith, G.R. and Stemberg, J.E. (2002) Curr Opin. Struct. Biol., 12, 28-35.
25. Smith, K.C. and Honig, B., (1994) Proteins: Struct. Funct. Genet., 18, 119-132.
26. Stoddard, B.L. and Koshland, D.E., Jr. (1993) Proc. Natl Acad. Sci. USA, 90, 1146-1153.
27. Takamatsu, Y. and Itai, A. (1998) Proteins: Struct. Funct. Genet., 33, 62-73.
28. Vajda, S., Weng, Z.P., Rosenfld, R. and DeLisi, C. (1994) Biochemistry, 33, 13977-13988.
29. Vajda, S., Weng, Z.P., and DeLisi, C. (1995) Protein Sci., 8, 1081-1092.
30. Vajda, S., Sippl, M., Novotny, J. (1997) Curr. Opin. Struct. Biol., 2, 222-228.
31. Weng, Z.P., DeLisi, C. and Vajda, S. (1997) Protein Sci., 6, 1976-1984.
32. Xu, D., Lin, S.L. and Nussinov, R. (1997) J. Mol. Biol., 265, 68-84.
33. Zhang, C., Vasmatzis, G., Cornette, J.L. and DeLisi, C. (1997) J. Mol. Biol., 267, 707-726.