Molecular modelling probes: Docking and scoring

Biochemical Society Transactions

Volumn 31, Issue 5, 2003, Pages 980-984

  Kroemer, R T ^a  

^a PFIZER INC   (United States)

Author keywords

Affinity prediction; Molecular interaction; Pose prediction

Indexed keywords

CARBONATE DEHYDRATASE II; DOCKING PROTEIN; LIGAND; PROTEIN; PROTEIN TYROSINE PHOSPHATASE; PROTEIN TYROSINE PHOSPHATASE 1B; UNCLASSIFIED DRUG;

ALGORITHM; BINDING AFFINITY; BINDING SITE; COMPARATIVE STUDY; CONFERENCE PAPER; LIGAND BINDING; MOLECULAR MODEL; MOLECULAR PROBE; PRIORITY JOURNAL; PROTEIN INTERACTION; SCORING SYSTEM; STATISTICAL ANALYSIS;

EID: 0142153340     PISSN: 03005127     EISSN: None     Source Type: Journal    
DOI: 10.1042/bst0310980     Document Type: Conference Paper

References (45)

1. Kroemer, R.T. (2001) in Protein-Ligand Interactions: Structure and Spectroscopy (Harding, S.E. and Chowdhry, B.Z., eds), pp. 99-121, Oxford University Press, New York
2. Proteins: Struct. Funct. Genet. (2001) 45 (55), 1-199
3. Peitsch, M.C., Schwede, T., Diemand, A. and Guex, N. (2002) in Current Topics in Computational Molecular Biology (Jiang, T., Xu, Y. and Zhang, M.Q., eds), pp. 449-466, MIT Press, Cambridge, MA
4. Zimmer, R. and Lengauer, T. (2002) in Bioinformatics - from Genomes to Drugs (Lengauer, T., ed.), pp. 237-313, Wiley-VCH, New York
5. Willis, R.C. (2002) Mod. Drug Disc. 5, 28-34
6. Sotriffer, C. and Klebe, G. (2002) Farmaco 57, 243-251
7. Bitetti-Putzer, R., Joseph-McCarthy, D., Hogle, J.M. and Karplus, M. (2001) J. Comput. Aided Mol. Design 15, 935-960
8. Murcko, M.A. (1997) in Practical Application of Computer-Aided Drug Design (Charifson, P.S., ed.), pp. 304-354, Marcel Dekker, New York
9. Klebe, G. (2000) J. Mol. Med. 78, 269-281
10. Kubinyi, H. (2002) Quant. Struct. Act. Relat. 21, 348-356
11. Müller, G. (2002) Quant. Struct. Act. Relat. 21, 391-396
12. Schneider, G. and Böhm, H.-J. (2002) Drug Discovery Today 7, 64-70
13. Waszkowycz, B. (2002) Curr. Opin. Drug Discovery Dev. 5, 407-413
14. Toledo-Sherman, L.M. and Chen, D. (2002) Curr. Opin. Drug Discovery Dev. 5, 414-421
15. Muegge, I. and Rarey, M. (2001) Rev. Comput. Chem. 17, 1-60
16. Virtual Screening for Bioactive Molecules (2000) (Böhm, H.-J. and Schneider, G., eds), Wiley-VCH, Weinheim
17. Doman, T.N., McGovern, S.L., Witherbee, B.J., Kasten, T.P., Kurumbail, R., Stallings, W.C., Connolly, D.T. and Shoichet, B.K. (2002) J. Med. Chem. 45, 2213-2221
18. Verkhivker, G.M., Bouzida, D., Gehlhaar, D.K., Rejto, P.A., Arthurs, S., Colson, A.B., Freer, S.T., Larson, V., Luty, B.A., Marrone, T. and Rose, P.W. (2000) J. Comput. Aided Mol. Design 14, 731-751
19. Stahl, M. and Rarey, M. (2001) J. Med. Chem. 44, 1035-1042
20. Welch, W., Ruppert, J. and Jain, A.J. (1996) Chem. Biol. 3, 449-462
21. Ewing, T.J.A. and Kuntz, I.D. (1997) J. Comp. Chem. 18, 1176-1189
22. Rarey, M., Kramer, B., Lengauer, T. and Klebe, G. (1996) J. Mol. Biol. 261, 470-489
23. Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E., Belew, R.K. and Olson, A.J. (1998) J. Comp. Chem. 19, 1639-1662
24. Jones, G., Willett P., Glen, R.C., Leach, A.R. and Taylor, R. (1997) J. Mol. Biol. 267, 727-748
25. Totrov, M. and Abagyan, R. (1997) Proteins Struct. Funct. Genet. S1, 215-220
26. McMartin, C. and Bohacek, R.S. (1997) J. Comput. Aided Mol. Design 11, 333-344
27. Osterberg, F., Morris, G.M., Sanner, M.F. and Olson, A.J. (2002) Proteins Struct. Funct. Genet. 46, 34-40
28. Claussen, H., Buning, C., Rarey, M. and Lengauer T. (2001) J. Mol. Biol. 308, 377-395
29. Luty, B.A., Wasserman, Z.R., Stouten, P.F.W., Hodge, C.N., Zacharias, M. and McCammon, J.A. (1995) J. Comp. Chem. 16, 454-464
30. Abagyan, R. (1992) J. Mol. Biol. 225, 519-532
31. Smellie, A., Teig, S.L. and Towbin, P. (1995) J. Comp. Chem. 16, 171-187
32. Tabu Search (1998) (Glover, F.W., ed), Kluwer Academic Publishers, Boston
33. Murcko, M.A. and Stouten, P.F.W. (1997) in Practical Application of Computer-Aided Drug Design (Charifson, P.S., ed.), p. 355, Marcel Dekker, New York
34. Gohlke, H. and Klebe, G. (2001) Curr. Opin. Struct. Biol. 11, 231-235
35. Böhm, H.-J. and Stahl, M. (1999) Med. Chem. Res. 9, 445-462
36. Stahl, M. (2000) Persp. Drug Disc. Des. 20, 83-98
37. Muegge, I. and Martin Y.C. (1999) J. Med. Chem. 42, 791-804
38. Gohlke, H., Hendlich, M. and Klebe, G. (2000) J. Mol. Biol. 295, 337-356
39. Charifson, P.S., Corkery, J.J., Murcko, M.A. and Walters, W.P. (1999) J. Med. Chem. 42, 5100-5109
40. Terp, G.E., Johansen, B.N., Christensen, I.T. and Jørgensen, F.S. (2001) J. Med. Chem. 44, 2333-2343
41. Gohlke, H. and Klebe, G. (2002) Angew. Chem. Int. Ed. 41, 2644-2676
42. Grüneberg, S., Wendt, B. and Klebe, G. (2001) Angew. Chem. Int. Ed. 40, 389-393
43. Grüneberg, S., Stubbs, M.J. and Klebe, G. (2002) J. Med. Chem. 45, 3588-3602
44. Lorber, D.M. and Shoichet, B.K. (1998) Protein Sci. 7, 938-950
45. Meng, E.C., Shoichet, B.K. and Kuntz, I.D. (1992) J. Comp. Chem. 13, 505-524