Comparison of two implementations of the incremental construction algorithm in flexible docking of thrombin inhibitors

Journal of Computer-Aided Molecular Design

Volumn 13, Issue 2, 1999, Pages 167-183

  Knegtel, Ronald M A ^a   Bayada, Denis M ^a   Engh, Richard A ^b   Von Der Saal, Wolfgang ^c   Van Geerestein, Vincent J ^a   Grootenhuis, Peter D J ^a,d  

^a NV ORGANON   (Netherlands)

^b MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^c F HOFFMANN LA ROCHE LTD   (Switzerland)

^d Formerly CombiChem Inc   (United States)

Author keywords

Flexible docking; Incremental construction algorithm; Scoring function; Structure based drug design; Thrombin

Indexed keywords

DOCKS; ENZYMES; HYDRAULIC STRUCTURES;

CHEMICAL CLASS; CONSTRUCTION ALGORITHMS; FLEXIBLE DOCKING; INCREMENTAL CONSTRUCTION; INCREMENTAL CONSTRUCTION ALGORITHM; SCORING FUNCTIONS; SCORING METHODS; STRUCTURE BASED DRUG DESIGNS; THROMBIN; THROMBIN INHIBITORS;

CONFORMATIONS;

THROMBIN INHIBITOR;

ARTICLE; BINDING SITE; DATA BASE; DRUG BINDING; DRUG CONFORMATION; DRUG DESIGN; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL;

EID: 0033065220     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1008014604433     Document Type: Article

References (47)

1. Kuntz, I.D., Science, 257 (1992) 107.
2. Kuntz, I.D., Meng, E.C. and Shoichet, B.K., Acc. Chem. Res., 27 (1994) 117.
3. Charifson, P.S. and Kuntz, I.D., In Charifson, P.S. (Ed.) Practical Application of Computer-Aided Drug Design, Marcel Dekker, New York, NY, 1997, pp. 1-38.
4. Grootenhuis, P.D.J., Knegtel, R.M.A., Heikoop, J.C. and van Boeckel, C.A.A., In van der Goot (Ed.) Trends in Drug Research II, Elsevier, Amsterdam, 1998, pp. 7-14.
5. Lorber, D.M. and Shoichet, B.K., Protein Sci., 7 (1998) 938.
6. Rosenfeld, R., Vajda, S. and DeLisi, Annu Rev. Biophys. Biomol. Struct., 24 (1995) 677.
7. Lambert, M.H., In Charifson, P.S. (Ed.) Practical Application of Computer-Aided Drug Design, Marcel Dekker, New York, NY, 1997, pp. 243-303.
8. Jones, G., Willett, P., Glen, R.C., Leach, A.R. and Taylor, R., J. Mol. Biol., 267 (1997) 727.
9. Goodsell, D.S., Morris, G.M. and Olson, A.J., J. Mol. Recog., 9 (1996) 1.
10. Leach, A.R. and Kuntz, I.D., J. Comput. Chem., 13 (1992) 730.
11. Rarey, M., Kramer, B., Lengauer, T. and Klebe, G., J. Mol. Biol., 261 (1996) 470.
12. Makino, S. and Kuntz, I.D., J. Comput. Chem., 18 (1997) 1812.
13. Welch, W., Ruppert, J. and Jain, A.J., Chem. Biol., 3 (1996) 449.
14. Ewing, T.J.A. and Kuntz, I.D., J. Comput. Chem., 18 (1997) 1175.
15. Rarey, M., Kramer, B. and Lengauer, T., J. Comput.-Aided Mol. Design, 10 (1997) 369.
16. Kramer, B., Rarey, M. and Lengauer, T., Proteins Struct. Funct. Genet. (Suppl. 1) (1997) 221.
17. Böhm, H.-J., J. Comput.-Aided Mol. Design, 8 (1994) 243.
18. Weiner, S.J., Kollman, P.A., Nguyen, D.T. and Case, D.A., J. Comput. Chem., 7 (1986) 230.
19. Meng, E.C., Shoichet, B.K. and Kuntz, I.D., J. Comput. Chem., 13 (1992) 505.
20. Böhm, H.-J. and Klebe, G., Angew. Chem., Int. Ed. Engl., 35 (1996) 2588.
21. Knegtel, R.M.A. and Grootenhuis, P.D.J., In Kubinyi, H., Folkers, G. and Martin, Y. (Eds.) 3D QSAR in Drug Design. Recent Advances, Kluwer, Dordrecht, 1998, pp. 99-114.
22. Dixon, J.S., Proteins Struct. Funct. Genet. (Suppl. 1) (1997) 198.
23. Grootenhuis, P.D.J. and Karplus, M., J. Comput.-Aided Mol. Design, 10 (1996) 1.
24. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.T.J., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M., J. Mol. Biol., 112 (1977) 535.
25. Engh, R.A., Brandstetter, H., Sucher, G., Eichinger, A., Baumann, U., Bode, W., Huber, R., Poll, T., Rudolph, R. and von der Saal, W., Structure, 4 (1996) 1353.
26. Von der Saal, W., Kucznierz, R., Leinert, H. and Engh, R.A., Bioorg. Med. Chem. Lett., 7 (1997) 1283.
27. Brandstetter, H., Turk, D., Hoeffken, W., Grosse, D., Sturzebecher, J., Martin, P.D., Edwards, B.F.P. and Bode, W., J. Mol. Biol., 226 (1992) 1085.
28. Banner, D.W. and Hadvary, P., J. Biol. Chem., 266 (1991) 20085.
29. Bode, W. and Turk, J., Eur. J. Biochem., 193 (1990) 175.
30. Sadowski, J., Gasteiger, J. and Klebe, G., J. Chem. Inf. Comput. Sci., 34 (1994) 1000.
31. Rusinko, A., Sheridan, R.P., Nilakantan, R., Haraki, K.S., Bauman, N. and Venkataraghavan, R., J. Chem. Inf. Comput. Sci., 29 (1989) 251.
32. Gasteiger, J. and Marsili, M., Tetrahedron Lett., 36 (1980) 3219.
33. McHugh, J., Algorithmic Graph Theory, Prentice-Hall, 1990, pp. 90-114.
34. Bayada et al., J. Chem. Inf. Comput. Sci., submitted.
35. Bauknecht, H., Zell, A., Bayer, H., Levi, R, Wagener, M., Sadowski, J. and Gasteiger, J., J. Chem. Inf. Comput. Sci., 36 (1996) 1205.
36. Grootenhuis, P.D.J. and van Galen, P.J.M., Acta Crystallogr., D51 (1995) 560.
37. Bursi, R.B. and Grootenhuis, P.D.J., J. Comput.-Aided Mol. Design (1999) in press.
38. Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R. and Ferrin, T.E., J. Mol. Biol., 161 (1982) 269.
39. Ewing, T. (Ed.) DOCK Version 4.0 Manual, Regents of the University of California, San Francisco, CA, 1997.
40. Kearsley, S.K., Underwood, D.J., Sheridan, R.P. and Miller, M.D., J. Comput-Aided Mol. Design, 8 (1994) 565.
41. Miller, M.D., Kearsley, S.K., Underwood, D.J. and Sheridan, R.P., J. Comput.-Aided Mol. Design, 8 (1994) 153.
42. Knegtel, R.M.A., Kuntz, I.D. and Oshiro, C.M., J. Mol. Biol., 266 (1997) 424.
43. Todeschini, R., Lasagni, M. and Marengo, E., J. Chemometrics, 8 (1994) 263.
44. Todeschini, R., Gramatica, P., Provenzani, R. and Marengo, E., Chemometr. Intell. Lab. Syst., 27 (1995) 221.
45. Todeschini, R. and Gramatica, P., Quant. Struct.-Act. Relat., 16 (1997) 113.
46. Broto, P., Moreau, G. and Vandycke, C., Eur. J. Med. Chem., 19 (1984) 66.
47. Broto, P., Moreau, G. and Vandycke, C., Eur. J. Med. Chem., 19 (1984) 79.