Comparative study of several algorithms for flexible ligand docking

Journal of Computer-Aided Molecular Design

Volumn 17, Issue 11, 2003, Pages 755-763

  Bursulaya, Badry D ^a   Totrov, Maxim ^a   Abagyan, Ruben ^a   Brooks III, Charles L ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

AutoDock; DOCK; FlexX; Gold; ICM

Indexed keywords

COMPLEXATION; DOCKS; GOLD; HYDRAULIC STRUCTURES; PROTEINS;

AUTODOCK; COMPARATIVE ASSESSMENT; COMPARATIVES STUDIES; DATABASE SCREENINGS; FLEXIBLE LIGANDS; FLEXX; GOLD; ICM; LIGAND DOCKING; MOLECULAR DOCKING;

LIGANDS;

ARABINOSE; BINDING PROTEIN; CARBONATE DEHYDRATASE II; CARBOXYPEPTIDASE; CYTOCHROME P450; LIGAND; RIBONUCLEASE; SIALIDASE; THERMOLYSIN; THROMBIN; TRYPSIN;

ACCURACY; ALGORITHM; ARTICLE; COMPARATIVE STUDY; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; GENE LIBRARY; GENETIC ALGORITHM; INFORMATION PROCESSING; LIGAND BINDING; PRIORITY JOURNAL; PROTEIN BINDING; QUALITY CONTROL; SCORING SYSTEM; SCREENING;

EID: 1842431537     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/B:JCAM.0000017496.76572.6f     Document Type: Article

References (31)

1. Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R. and Ferrin, T.E., J. Mol. Biol., 161 (1982) 269.
2. Roche, O., Kiyama, R. and Brooks, C.L., III, J. Med. Chem., 44 (2001) 3592.
3. Kearsley, S.K., Underwood, D.J., Sheridan, R.P., and Miller, M.D., J. Comput.-Aided Mol. Des., 8 (1994) 565.
4. Leach, A.R., J. Mol. Biol., 235 (1994) 345.
5. Welch, W., Ruppert, J. and Jain, A.N., Chem. Biol., 3 (1996) 449.
6. Ewing, T.J.A. and Kuntz, I.D., J. Comput. Chem., 18 (1997) 1176.
7. Rarey, M., Kramer, B., Lengauer, T. and Klebe, G., J. Mol. Biol., 261 (1996) 470.
8. Goodford, P.J., J. Med. Chem., 28 (1985) 849.
9. Miller, M.D., Kearsley, S.K., Underwood, D.J. and Sheridan, R.P., J. Comput.-Aided Mol. Des., 8 (1994) 153.
10. Momany, F.A., McGuire, R.F., Burgess, A.W. and Scheraga, H.A., J. Phys. Chem., 79 (1975) 2361.
11. Goodsell, D.S. and Olson, A.J., Proteins, 8 (1990) 195.
12. Mazur, A.K. and Abagyan, R.A., J. Biomol. Struct. Dyn., 6 (1989) 815.
13. Abagyan, R. and Argos, P., J. Mol. Biol., 225 (1992) 519.
14. Abagyan, R., Totrov, M. and Kuznetsov, D., J. Comput. Chem., 15 (1994) 488.
15. Vieth, M., Hirst, J.D., Dominy, B.N., Daigler, H. and Brooks, C.L., III, J. Comput. Chem., 19 (1998) 1623.
16. Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E., Belew, R.K. and Olson, A.J., J. Comput. Chem., 19 (1998) 1639.
17. Liu, M. and Wang, S., J. Comput.-Aided Mol. Des., 13 (1999) 435.
18. Totrov, M. and Abagyan, R., Proteins, Suppl 1 (1997) 215.
19. Totrov, M. and Abagyan, R. In: Protein-ligand Docking as an Energy Optimization Problem. The Thermodynamics of Receptor-Inhibitor Interactions, ed. R.B. Raffa. Wiley and Sons, New York, 2000.
20. McMartin, C. and Bohacek, R.S., J. Comput.-Aided Mol. Des., 11 (1997) 333.
21. Jones, G., Willett, P. and Glen, R.C., J. Mol. Biol., 245 (1995) 43.
22. Jones, G., Willett, P., Glen, R.C., Leach, A.R. and Taylor, R., J. Mol. Biol., 267 (1997) 727.
23. Wu, G., Robertson, D.H., Brooks, C.L., III, and Vieth, M., J. Comput. Chem., 24 (2003) 1549.
24. Vieth, M., Hirst, J.D., Kolinski, A. and Brooks, C.L., III, J. Comput. Chem., 19 (1998) 1612.
25. Ha, S., Andreani, R., Robbins, A. and Muegge, I., J. Comput.-Aided Mol. Des., 14 (2000) 435.
26. Charifson, P.S., Corkery, J.J., Murcko, M.A. and Walters, W.P., J. Med. Chem., 42 (1999) 5100.
27. Diller, D.J. and Verlinde, L.M.J., J. Comput. Chem., 20 (1999) 1740.
28. Knegtel, R.M., Bayada, D.M., Engh, R.A., von der Saal, W., van Geerestein, V.J. and Grootenhuis, P.D., J. Comput.-Aided Mol. Des., 13 (1999) 167.
29. Bissantz, C., Folkers, G. and Rognan, D., J. Med. Chem., 43 (2000) 4759.
30. Kramer, B., Rarey, M. and Lengauer, T., Proteins, 37 (1999) 228.
31. Halgren, T.A., J. Comput. Chem., 17 (1995) 490-641.