Computer simulations of ligand-protein binding with ensembles of protein conformations: A monte carlo study of HIV-1 protease binding energy landscapes

International Journal of Quantum Chemistry

Volumn 72, Issue 1, 1999, Pages 73-84

  Bouzida, Djamal ^a   Rejto, Paul A ^a   Arthurs, Sandra ^a   Colson, Anthony B ^a   Freer, Stephan T ^a   Gehlhaar, Daniel K ^a   Larson, Veda ^a   Luty, Brock A ^a   Rose, Peter W ^a   Verkhivker, Gennady M ^a  

^a AGOURON PHARMACEUTICALS INC   (United States)

Author keywords

Conformational substates; Ensemble of protein conformations; Free energy profiles; Molecular recognition; Monte Carlo docking

Indexed keywords

EID: 0002133819     PISSN: 00207608     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-461X(1999)72:1<73::AID-QUA7>3.0.CO;2-O     Document Type: Article

References (14)

1. Kuntz, I. D. Science 1992, 257, 1078-1082.
2. Miller, D. W.; Dill, K. A. Protein Sci 1997, 6, 2166-2179.
3. Frauenfelder, H.; Sliger, S. G.; Wolynes, P. Science 1991, 254, 1598-1603.
4. Frauenfelder, H. Nature Struct Biol 1995, 2, 821-823.
5. Leeson, D. T.; Wiersma, D. A. Nature Struct Biol 1995, 2, 848-851.
6. Elber, R.; Karplus, M. Science 1987, 235, 318-321.
7. Noguti, T.; Go, N. Proteins 1989, 5, 97-103.
8. Go, N.; Noguti, T. Chem Scripta 1989, 29A, 151-164.
9. Troyer, J. M.; Cohen, F. E. Proteins 1995, 23, 97-110.
10. Bryngelson, J. D.; Onuchic, J. N.; Socci, N. D.; Wolynes, P. G. Proteins 1995, 21, 167-195.
11. Dill, K. A.; Bromberg, S.; Yue, K.; Fiebig, K. M.; Yee, D. P.; Thomas, P. D.; Chan, H. S. Protein Sci 1995, 4, 561-602.
12. Rejto, P. A.; Freer, S. T. Prog Biophys Molec Biol 1996, 66, 167-196.
13. Mirny, L. A.; Abkevich, V.; Shakhnovich, E. I. Folding & Design 1996, 1, 103-116.
14. Veitshans, T.; Klimov, D. K.; Thirumalai, D. Folding & Design 1997, 2, 1-22.