Representing receptor flexibility in ligand docking through relevant normal modes

Journal of the American Chemical Society

Volumn 127, Issue 26, 2005, Pages 9632-9640

  Cavasotto, Claudio N ^a   Kovacs, Julio A ^b   Abagyan, Ruben A ^b  

^a MOLSOFT LLC   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; CHEMICAL BONDS; COMPLEXATION; DEFORMATION; NATURAL FREQUENCIES; SCREENING;

LIGAND DOCKING; PROTEIN KINASE; RECEPTOR FLEXIBILITY; VIRTUAL SCREENING;

ENZYME KINETICS;

CYCLIC AMP DEPENDENT PROTEIN KINASE; LIGAND; PROTEIN KINASE; RECEPTOR;

ALGORITHM; ARTICLE; CONFORMATION; DRUG RESEARCH; LIGAND BINDING; LIGAND DOCKING; METHODOLOGY; RECEPTOR BINDING; RECEPTOR FLEXIBILITY; SCREENING; TECHNIQUE; VIRTUAL SCREENING;

ALGORITHMS; COMPUTER SIMULATION; LIGANDS; PROTEIN BINDING; PROTEIN KINASES; RECEPTORS, CELL SURFACE;

EID: 21644473891     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja042260c     Document Type: Article

References (48)

1. Amzel, L. M. Curr. Opin. Biotechnol. 1998, 9, 366-369.
2. Shoichet, B. K.; McGovern, S. L.; Wei, B. Q.; Irwin, J. J. Curr. Opin. Chem. Biol. 2002, 6, 439-446.
3. Najmanovich, R.; Kuttner, J.; Sobolev, V.; Edelman, M. Proteins: Struct., Funct. Bioinf. 2000, 39, 261-268.
4. Erickson, J. A.; Jalaie, M.; Robertson, D. H.; Lewis, R. A.; Vieth, M. J. Med. Chem. 2004, 47, 45-55.
5. Davis, A. M.; Teague, S. J. Angew. Chem., Int. Ed. 1999, 38, 736-749.
6. Teague, S. J. Nat. Rev. Drug Discov. 2003, 2, 527-541.
7. Cavasotto, C. N.; et al. J. Med. Chem. 2004, 47, 4360-4372.
8. Jiang, F.; Kim, S. H. J. Mol. Biol. 1991, 219, 79-102.
9. Leach, A. R. J. Mol. Biol. 1994, 235, 345-356.
10. Jones, G.; Willett, P.; Glen, R. C. J. Mol. Biol. 1995, 245, 43-53.
11. Carlson, H. A. Curr. Pharm. Des. 2002, 8, 1571-1578.
12. Teodoro, M. L.; Kavraki, L. E. Curr. Pharm. Des. 2003, 9, 1635-1648.
13. Cavasotto, C. N.; Orry, A. J. W.; Abagyan, R. A. Curr. Comput.-Aided Drug Des. 2005. in press.
14. Cavasotto, C. N.; Abagyan, R. J. Mol. Biol. 2004, 337, 209-225.
15. Knegtel, R. M.; Kuntz, I. D.; Oshiro, C. M. J. Mol. Biol. 1997, 266, 424-40.
16. Claussen, H.; Buning, C.; Rarey, M.; Lengauer, T. J. Mol. Biol. 2001, 308, 377-395.
17. Wei, B. Q.; Weaver, L. H.; Ferrari, A. M.; Matthews, B. W.; Shoichet, B. K. J. Mol. Biol. 2004, 337, 1161-1182.
18. Lin, J. H.; Perryman, A. L.; Schames, J. R.; McCammon, J. A. J. Am. Chem. Soc. 2002, 124, 5632-5633.
19. Carlson, H. A.; Masukawa, K. M.; Rubins, K.; Bushman, F. D.; Jorgensen, W. L.; Lins, R. D.; Briggs, J. M.; McCammon, J. A. J. Med. Chem. 2000, 43, 2100-2014.
20. Meagher, K. L.; Carlson, H. A. J. Am. Chem. Soc. 2004, 126, 13276-13281.
21. Keserû, G. M.; Kolossváry, I. J. Am. Chem. Soc. 2001, 123, 12708-12709.
22. Tatsumi, R.; Fukunishi, Y.; Nakamura, H. J. Comput. Chem. 2004, 25, 1995-2005.
23. Ma, B.; Kumar, S.; Tsai, C. J.; Nussinov, R. Protein Eng. 1999, 12, 713-720.
24. Tsai, C. J.; Kumar, S.; Ma, B.; Nussinov, R. Protein Sci. 1999, 8, 1181-1190.
25. Bosshard, H. R. News Physiol. Sci. 2001, 16, 171-173.
26. Fischer, E. Ber. Dtsch. Chem. Ges. 1894, 27, 2984-2993.
27. Ikeguchi, M.; Ueno, J.; Sato, M.; Kidera, A. Phys. Rev. Lett. 2005, 94, 078102.
28. Noguti, T.; Gō, N. Nature 1982, 296, 776-778.
29. Noguti, T.; Gō, N. Biopolymers 1985, 24, 527-546.
30. Hayward, S.; Gō, N. Annu. Rev. Phys. Chem. 1995, 46, 223-250.
31. Tirion, M. M. Phys. Rev. Lett. 1996, 77, 1905-1908.
32. Hinsen, K. Proteins: Struct., Funct. Bioinf. 1998, 33, 417-429.
33. Bahar, T.; Atilgan, A. R.; Erman, B. Fold. Des. 1997, 2, 173-181.
34. Delarue, M.; Dumas, P. Proc. Natl. Acad. Sci. 2004, 101, 6957-6962.
35. Abagyan, R. Protein structure prediction by global energy optimization. In Computer simulation of biomolecular systems, Vol. 3; van Gunsteren, W., Weiner, P., Wilkinson, A., Eds.; Kluwer/Escom: Dordrecht, The Netherlands, 1997.
36. Cavasotto, C. N.; Orry, A. J. W.; Abagyan, R. A. Proteins: Struct., Funct. Bioinf. 2003, 51, 423-433.
37. Abagyan, R.; Argos, P. J. Mol. Biol. 1992, 225, 519-532.
38. Totrov, M.; Abagyan, R. Biopolymers 2001, 60, 124-133.
39. Abagyan, R.; Totrov, M.; Kuznetsov, D. J. Comput. Chem. 1994, 15, 488-506.
40. Totrov, M.; Abagyan, R. Derivation of sensitive discrimination potential for virtual ligand screening. In RECOMB '99: Proceedings of the Third Annual International Conference on Computational Molecular Biology; Istrail, S., Pevzner, P., Waterman, M., Eds.; Associaton for Computer Machinery: New York/Lyon, France, 1999.
41. Totrov, M.; Abagyan, R. Protein-ligand docking as an energy optimization problem. In Drug-receptor thermodynamics: Introduction and experimental applications; Raffa, R., Ed.; John Wiley and Sons: New York, 2001.
42. Halgren, T. J. Comput. Chem. 1995, 17, 490-641.
43. Némethy, G.; Gibson, K. D.; Palmer, K. A.; Yoon, C.; Paterlini, M. G.; Zagari, A.; Rumsey, S.; Scheraga, H. A. J. Phys. Chem. 1992, 96, 6472-6484.
44. Abagyan, R.; Totrov, M. J. Mol. Biol. 1994, 235, 983-1002.
45. Metropolis, N.; Rosenbluth, A.; Rosenbluth, N.; Teller, A.; Teller, E. J. Chem. Phys. 1953, 21, 1087-1092.
46. Anderson, E.; et al. LAPACK Users' Guide, 3rd ed.; Society for Industrial and Applied Mathematics: Philadelphia, PA, 1999.
47. Brooks, B. R.; Janežič, D.; Karplus, M. J. Comput. Chem. 1995, 16, 1522-1542.
48. Kovacs, J. A.; Chacón, P.; Abasyan, R. Proteins: Struct., Fund., Bioinf. 2004, 56, 661-668.