A comparison of heuristic search algorithms for molecular docking

Journal of Computer-Aided Molecular Design

Volumn 11, Issue 3, 1997, Pages 209-228

  Westhead, David R ^a,b   Clark, David E ^a,c   Murray, Christopher W ^a  

^a Proteus Molecular Design Ltd   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c SANOFI   (France)

Author keywords

Evolutionary algorithms; Ligand protein docking; Molecular recognition; Simulated annealing; Tabu search

Indexed keywords

GENETIC ALGORITHMS; HEURISTIC ALGORITHMS; LEARNING ALGORITHMS; LIGANDS; MOLECULAR RECOGNITION; PROTEINS; SIMULATED ANNEALING;

HEURISTIC SEARCH ALGORITHMS; LIGAND SYSTEM; LIGAND-PROTEIN DOCKING; MOLECULAR DOCKING; POTENTIAL FUNCTION; PROTEIN DOCKING; PROTEIN LIGANDS; RANDOM SEARCHES; SEARCH PROCEDURES; TABU SEARCH ALGORITHMS;

TABU SEARCH;

ARGATROBAN; AZEPINE DERIVATIVE; DIHYDROFOLATE REDUCTASE; DIPEPTIDE; LIGAND; METHOTREXATE; N(ALPHA) (2 NAPHTHYLSULFONYLGLYCYL) 4 AMIDINOPHENYLALANINE PIPERIDIDE; N(ALPHA)-(2-NAPHTHYLSULFONYLGLYCYL)-4-AMIDINOPHENYLALANINE PIPERIDIDE; PIPECOLIC ACID DERIVATIVE; PIPERIDINE DERIVATIVE; PROTEINASE; SIALIDASE; THROMBIN; XK 263;

ALGORITHM; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; MACROMOLECULE; PROTEIN BINDING; STRUCTURE ACTIVITY RELATION; THERMODYNAMICS;

ALGORITHMS; AZEPINES; BINDING SITES; COMPUTER SIMULATION; DIPEPTIDES; HIV PROTEASE; LIGANDS; MACROMOLECULAR SUBSTANCES; METHOTREXATE; MODELS, MOLECULAR; NEURAMINIDASE; PIPECOLIC ACIDS; PIPERIDINES; PROTEIN BINDING; SOFTWARE DESIGN; STRUCTURE-ACTIVITY RELATIONSHIP; TETRAHYDROFOLATE DEHYDROGENASE; THERMODYNAMICS; THROMBIN;

EID: 0031135364     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1007934310264     Document Type: Review

References (59)

1. Blaney, J.M. and Dixon, J.S., Perspect. Drug Discov. Design, 1 (1993) 301.
2. Jones, G. and Willett, P., Curr. Opin. Biotechnol., 6 (1995) 652.
3. Lybrand, T.P., Curr. Opin. Struct. Biol., 5 (1995) 224.
4. Rosenfeld, R., Vajda, S. and Delisi, C., Annu. Rev. Biophys., Biomol. Struct., 24 (1995) 677.
5. Gschwend, D.A., Good, A.C. and Kuntz, I.D., J. Mol. Recog., 9 (1996) 175.
6. Lengauer, T. and Rarey, M., Curr. Opin. Struct. Biol., 6 (1996) 402.
7. Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R. and Ferrin, T.E., J. Mol. Biol., 161 (1982) 269.
8. Goodsell, D.S. and Olson, A.J., Proteins Struct. Funct. Genet., 8 (1990) 195.
9. Yamada, M. and Itai, A., Chem. Pharm. Bull., 41 (1993) 1200.
10. Yamada, M. and Itai, A., Chem. Pharm. Bull., 41 (1993) 1203.
11. Leach, A.R., J. Mol. Biol., 235 (1994) 345.
12. Miller, M.D., Kearsley, S.K., Underwood, D.J. and Sheridan, R.P., J. Comput.-Aided Mol. Design, 8 (1994) 153.
13. Clark, K.P. and Ajay, J. Comput. Chem., 16 (1995) 1210.
14. Gehlhaar, D.K., Verkhivker, G.M., Rejto, P.A., Sherman, C.J., Fogel, D.B., Fogel, L.J. and Freer, S.T., Chem. Biol., 2 (1995) 317.
15. Gehlhaar, D.K., Verkhivker, G.M., Rejto, P.A., Fogel, D.B., Fogel, L.J. and Freer, S.T., In McDonnell, J.R., Reynolds, R.G. and Fogel, D.B. (Eds.) Evolutionary Programming IV (Proceedings of the Fourth Annual Conference on Evolutionary Programming), MIT Press, Cambridge, MA, U.S.A., 1995, pp. 615-627.
16. Jones, G., Willett, P. and Glen, R.C., J. Mol. Biol., 245 (1995) 43.
17. Judson, R.S., Tan, Y.T., Mori, E., Melius, C., Jaeger, E.P., Treasurywala, A.M. and Mathiowetz, A., J. Comput. Chem., 16 (1995) 1405.
18. Oshiro, C.M., Kuntz, I.D. and Dixon, J.S., J. Comput.-Aided Mol. Design, 9 (1995) 113.
19. Goodsell, D.S., Morris, G.M. and Olson, A.J., J. Mol. Recog., 9 (1996) 1.
20. Morris, G.M., Goodsell, D.S., Huey, R. and Olson, A.J., J. Comput.-Aided Mol. Design, 10 (1996) 293.
21. Rarey, M., Wefing, S. and Lengauer, T., J. Comput.-Aided Mol. Design, 10 (1996) 41.
22. Rarey, M., Kramer, B., Lengauer, T. and Klebe, G., J. Mol. Biol., 261 (1996) 470.
23. Welch, W., Ruppert, J. and Jain, A.N., Chem. Biol., 3 (1996) 449.
24. Abagyan, R.A., Totrov, M. and Kuznetsov, D., J. Comput. Chem., 15 (1994) 488.
25. Read, R.J., Hart, T.N., Cummings, M.D. and Ness, S.R., Supramol. Chem., 6 (1995) 135.
26. Verkhivker, G.M., Rejto, P.A., Gehlhaar, D.K. and Freer, S.T., Proteins Struct. Funct. Genet., 250 (1996) 342.
27. Kirkpatrick, S., Gelatt, C.D. and Vecchi, M.P., Science, 220 (1983) 671.
28. Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A.H. and Teller, E., J. Chem. Phys., 21 (1953) 1087.
29. Szu, H.H. and Hartley, R.L., Phys. Lett., A122 (1987) 157.
30. Fogel, D., Evolutionary Computation: Towards a New Philosophy of Machine Intelligence, IEEE Press, Piscataway, NJ, U.S.A., 1995, pp. 121-186.
31. Yao, X. and Liu, Y., In Fogel, L.J., Angeline, P.J. and Bäck, T. (Eds.) Evolutionary Programming V (Proceedings of the Fifth Annual Conference on Evolutionary Programming), MIT Press, Cambridge, MA, U.S.A., 1996, pp. 257-266.
32. Saravanan, N., Fogel, D.B. and Nelson, K.M., BioSystems, 36 (1995) 157.
33. Glover, F. and Laguna, M., In Reeves, C.R. (Ed.) Modern Heuristic Techniques for Combinatorial Problems, Blackwell, Oxford, U.K., 1993, pp. 70-150.
34. Cvijovic, D. and Klinowski, J., Science, 267 (1995) 664.
35. Kvasnička, V. and Pospíchal, J., J. Chem. Inf. Comput. Sci., 34 (1994) 1109.
36. Goodman, J.M. and Still, W.C., J. Comput. Chem., 12 (1991) 1110.
37. Huber, T., Torda, A. and Van Gunsteren, W.F., J. Comput.-Aided Mol. Design, 8 (1994) 695.
38. Smellie, A., Teig, S.L. and Towbin, P., J. Comput. Chem., 16 (1995) 171.
39. Goldberg, D.E., Genetic Algorithms in Search, Optimization, and Machine Learning, Addison-Wesley, Reading, MA, U.S.A., 1989.
40. Press, W.H., Teukolsky, S.A., Vetterling, W.T. and Flannery, B.P., Numerical Recipes in C: The Art of Scientific Computing, 2nd ed., Cambridge University Press, Cambridge, U.K., 1992, pp. 412-420.
41. Gardner, M.J. and Altman, D.G., Statistics with Confidence, British Medical Journal, Tavistock Square, London, U.K., 1989, pp. 74-76.
42. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M., J. Mol. Biol., 112 (1977) 535.
43. InsightII/Discover, v. 95.0, Molecular Simulations Inc., San Diego, CA, U.S.A., 1996.
44. Poornima, C.S. and Dean, P.M., J. Comput.-Aided Mol. Design, 9 (1995) 500.
45. Poornima, C.S. and Dean, P.M., J. Comput.-Aided Mol. Design, 9 (1995) 513.
46. Poornima, C.S. and Dean, P.M., J. Comput.-Aided Mol. Design, 9 (1995) 521.
47. Guida, W.C., Bohacek, R.S. and Erion, M.D., J. Comput. Chem., 13 (1992) 214.
48. Mayo, S.L., Olafson, B.D. and Goddard, W.A., J. Phys. Chem., 94 (1990) 8897.
49. Gehlhaar, D.K., private communication, 1996.
50. Gschwend, D.A. and Kuntz, I.D., J. Comput.-Aided Mol. Design, 10 (1996) 123.
51. Meza, J.C., Judson, R.S., Faulkner, T.R. and Treasurywala, A.M., J. Comput. Chem., 17 (1996) 1142.
52. Montoya, F. and Dubois, J.M., Europhys. Lett., 22 (1993) 79.
53. Kido, T., Takagi, K. and Nakanishi, M., Informatica, 18 (1994) 399.
54. Mahfoud, S.W. and Goldberg, D.E., Paral. Comput., 21 (1995) 1.
55. Tang, R.Y., Yang, S.Y., Li, Y., Wen, G. and Mei, T.M., IEEE Trans. Magnetics, 32 (1996) 1326.
56. Bolin, J.T., Filman, D.J., Matthews, D.A., Hamlin, R.C. and Kraut, J., J. Mol. Biol., 257 (1982) 13650.
57. Burmeister, W.P., Henrissat, B., Bosso, C., Cusack, S. and Ruigrok, R.W.H., Structure, 1 (1993) 19.
58. Lam, P.Y.S., Jadhav, P.K., Eyermann, C.J., Hodge, C.N., Ru, Y., Bacheler, L.T., Meek, J.L., Otto, M.J., Rayner, M.M., Wong, Y.N., Chang, C.-H., Weber, P.C., Jackson, D.A., Sharpe, T.R. and Erickson-Viitanen, S., Science, 263 (1994) 380.
59. Brandstetter, H., Turk, D., Hoeffken, H.W., Grosse, D., Stuerzebecher, J., Martin, P.D., Edwards, B.F.P. and Bode, W., J. Mol. Biol., 226 (1992) 1085.