Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4

Journal of Computer-Aided Molecular Design

Volumn 10, Issue 4, 1996, Pages 293-304

  Morris, Garrett M ^a   Goodsell, David S ^a   Huey, Ruth ^a   Olson, Arthur J ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Drug design; Inhibitor; Receptor; Simulated annealing

Indexed keywords

CONFORMATIONS; DEGREES OF FREEDOM (MECHANICS); HETEROGENEOUS NETWORKS; LIGANDS;

AUTODOCK; AUTOMATED DOCKING; DRUG DESIGN; ENERGY EVALUATION; FLEXIBLE LIGANDS; GRID BASED METHOD; INHIBITOR; MACROMOLECULAR TARGETS; PARALLEL APPLICATION; RECEPTOR;

SIMULATED ANNEALING;

AZEPINE DERIVATIVE; BACTERIAL PROTEIN; BENZAMIDINE; BENZAMIDINE DERIVATIVE; BIOTIN; CAMPHOR; CAMPHOR 5 MONOOXYGENASE; HEMAGGLUTININ; IMMUNOGLOBULIN F(AB) FRAGMENT; LIGAND; N ACETYLNEURAMINIC ACID; PHOSPHORYLCHOLINE; PROTEINASE; PROTEINASE INHIBITOR; STREPTAVIDIN; TRYPSIN; XK 263;

ARTICLE; CHEMISTRY; CLUSTER ANALYSIS; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; CONFORMATION; METABOLISM; PROTEIN BINDING; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

AZEPINES; BACTERIAL PROTEINS; BENZAMIDINES; BIOTIN; CAMPHOR; CAMPHOR 5-MONOOXYGENASE; CLUSTER ANALYSIS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; HEMAGGLUTININS; HIV PROTEASE; HIV PROTEASE INHIBITORS; IMMUNOGLOBULIN FAB FRAGMENTS; LIGANDS; MOLECULAR CONFORMATION; N-ACETYLNEURAMINIC ACID; PHOSPHORYLCHOLINE; PROTEIN BINDING; PROTEIN CONFORMATION; SOFTWARE; STREPTAVIDIN; TRYPSIN; USER-COMPUTER INTERFACE;

EID: 0030203710     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF00124499     Document Type: Article

References (31)

1. Blaney, J.M. and Dixon, J.S., Perspect. Drug Discov. Design, 1 (1993) 301.
2. Kuntz, I.D., Meng, E.C. and Shoichet, B.K., Acc. Chem. Res., 27 (1994) 117.
3. Rosenfeld, R., Vajda, S. and DeLisi, C., Annu. Rev. Biophys. Biomol. Struct, 24 (1995) 677.
4. Böhm, H.-J., J. Comput.-Aided Mol. Design, 6 (1992) 593.
5. Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R. and Ferrin, T.E., J. Mol. Biol., 161 (1982) 269.
6. Goodsell, D.S. and Olson, A.J., Proteins Struct. Funct. Genet., 8 (1990) 195.
7. Goodsell, D.S., Lauble, H., Stout, C.D. and Olson, A.J., Proteins Struct. Funct. Genet., 17 (1993) 1.
8. Lunney, E.A., Hagen, S.E., Domagala, J.M., Humblet, C., Kosinski, J., Tait, B.D., Warmus, J.S., Wilson, M., Ferguson, D., Hupe, D., Tummino, P.J., Baldwin, E.T., Bhat, T.N., Liu, B. and Erickson, J.W., J. Med. Chem., 37 (1994) 2664.
9. Vara Prasad, J.V.N., Para, K.S., Ortwine, D.F., Dunbar Jr., J.B., Ferguson, D., Tummino, P.J., Hupe, D., Tait, B.D., Domagala, J.M., Hunblet, C., Bhat, T.N., Liu, B., Guerin, D.M.A., Baldwin, E.T., Erickson, J.W. and Sawyer, T.K., J. Am. Chem. Soc., 116 (1994) 6989.
10. Stoddard, B.L. and Koshland, D.E., Nature, 358 (1992) 774.
11. Hart, W.E., Ph.D. Thesis, University of California, San Diego, CA, at 'ftp://ftp.cs.sandia.gov/pub/papers/wehart/thesis.ps.gz'.
12. Maillot, P.-G., In Glassner, A.S. (Ed.) Graphics Gems, Academic Press, New York, NY, 1990, pp. 498-515.
13. Watt, A. and Watt, M., Advanced Animation and Rendering Techniques - Theory and Practice, ACM Press, New York, NY, and Addison-Wesley Publishing Company, Wokingham, U.K., 1992.
14. Pattabiraman, N., Levitt, M., Ferrin, T.E. and Langridge, R., J. Comput. Chem., 6 (1985) 432.
15. Goodford, P.J., J. Med. Chem., 28 (1985) 849.
16. Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta Jr., S. and Weiner, P., J. Am. Chem. Soc., 106 (1984) 765.
17. Van der Waals, J.H., Lehrbuch der Thermodynamik, Part 1, Mass and Van Suchtelen, Leipzig, Germany, 1908.
18. Bashford, D. and Gerwert, K., J. Mol. Biol., 224 (1992) 473.
19. Bashford, D. and Karplus, M., Biochemistry, 29 (1990) 10219.
20. Gilson, M.K. and Honig, B., Nature, 330 (1987) 84.
21. Honig, B. and Nicholls, A., Science, 268 (1995) 1144.
22. Mehler, E.L. and Solmajer, T., Protein Eng., 4 (1991) 903.
23. Marquart, M., Walter, J., Deisenhofer, J., Bode, W. and Huber, R., Acta Crystallogr., Sect. B, 39 (1983) 480.
24. Poulos, T.L., Finzel, B.C. and Howard, A.J., J. Mol. Biol., 195 (1987) 687.
25. Padlan, E.A., Cohen, G.H. and Davies, D.R., Ann. Immunol. (Paris), Sect. C, 136 (1985) 271.
26. Weber, P.C., Ohlendorf, D.H., Wendolski, J.J. and Salemme, F.R., Science, 243 (1989) 85.
27. Lara, P.Y.S., Jadhav, P.K., Eyerman, C.J., Hodge, C.N., Ru, Y., Bacheler, L.T., Meek, J.L., Otto, M.J., Rayner, M.M., Wong, Y., Chang, C.-H., Weber, P.C., Jackson, D.A., Sharpe, T.R. and Erickson-Viitanen, S., Science, 263 (1994) 380.
28. Weis, W.I., Bruenger, A.T., Skehel, J.J. and Wiley, D.C., J. Mol. Biol., 212 (1990) 737.
29. McDonald, I.K. and Thornton, J.M., J. Mol. Biol., 239 (1994) 777.
30. Leach, A.R., Prout, C.K. and Dolata, D.P., J. Comput.-Aided Mol. Design, 4 (1990) 271.
31. Friedman, A.R., Roberts, V.A. and Tainer, J.A., Proteins Struct. Funct. Genet, 20 (1994) 15.