Software news and update a semiempirical free energy force field with charge-based desolvation

Journal of Computational Chemistry

Volumn 28, Issue 6, 2007, Pages 1145-1152

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

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

AutoDock4; Computational docking; Computer aided drug design; Desolvation models; Force fields; Prediction of free energy

Indexed keywords

AUTODOCK4; COMPUTATIONAL DOCKING; COMPUTER-AIDED DRUG DESIGN; DESOLVATION MODELS; FORCE FIELDS; PREDICTION OF FREE ENERGY;

COMPLEXATION; COMPUTER SIMULATION; COMPUTER SOFTWARE; FORCE CONTROL; LIGANDS; MOLECULAR DYNAMICS; THERMODYNAMICS;

FREE ENERGY;

LIGAND; PROTEIN; PROTEINASE; PROTEINASE INHIBITOR; WATER;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; DRUG DESIGN; ELECTRICITY; HYDROGEN BOND; MATHEMATICAL COMPUTING; METABOLISM; PROTEIN BINDING; PROTEIN DATABASE; THERMODYNAMICS;

ALGORITHMS; DATABASES, PROTEIN; DRUG DESIGN; ELECTROSTATICS; HIV PROTEASE; HIV PROTEASE INHIBITORS; HYDROGEN BONDING; LIGANDS; MATHEMATICAL COMPUTING; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN BINDING; PROTEINS; SOFTWARE; THERMODYNAMICS; WATER;

EID: 33947716119     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20634     Document Type: Article

References (21)

1. Schneider, G.; Bohm, H. J. Drug Discovery Today 2002, 7, 64.
2. Alvarez, J. C. Curr Opin Chem Biol 2004, 8, 365.
3. Oprea, T. I.; Matter, H. Curr Opin Chem Biol 2004, 8, 349.
4. Kitchen, D. B.; Decornez, H.; Furr, J. R.; Bajorath, J. Nat Rev Drug Discov 2004, 3, 935.
5. Mohan, V.; Gibbs, A. C.; Cummings, M. D.; Jaeger, E. P.; DesJarlais, R. L. Curr Pharm Des 2005, 11, 323.
6. Wang, W.; Donini, O.; Reyes, C. M.; Kollman, P. A. Annu Rev Biophys Biomol Struct 2001, 30, 211.
7. Halperin, I.; Ma, B.; Wolfson, H.; Nussinov, R. Proteins: Struct Funct Genet 2002, 47, 409.
8. Taylor, R. D.; Jewsbury, P. J.; Essex, J. W. J Comput Aided Mol Des 2002, 16, 151.
9. Brooijmans, N.; Kuntz, I. D. Annu Rev Biophys Biomol Struct 2003, 32, 335.
10. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. J Comput Chem 1998, 19, 1639.
11. Huey, R.; Goodsell, D. S.; Morris, G. M.; Olson, A. J. Lett Drug Des Discov 2004, 1, 178.
12. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ohio, C.; Alagona, G.; Profeta, S.; Weiner, P. J Am Chem Soc 1984, 106, 765.
13. Goodford, P. J. J Med Chem 1985, 28, 849.
14. Boobbyer, D. N. A.; Goodford, P. J.; McWhinnie, P. M.; Wade, R. C. J Med Chem 1989, 32, 1083.
15. Mehler, E. L.; Solmajer, T. Protein Eng 1991, 4, 903.
16. Stouten, P. F. W.; Frommel, C.; Nakamura, H.; Sander, C. Mol Simul 1993, 10, 97.
17. Wesson, L.; Eisenberg, D. Protein Sci 1992, 1, 227.
18. Sharp, K. A.; Nicholls, A.; Friedman, R.; Honig, B. Biochemistry 1991, 30, 9686.
19. Tetko, I. V.; Gasteiger, J.; Todeschini, R.; Mauri, A.: Livingstone. D. J.; Ertl, P.; Palyulin, V. A.; Radchenko, E. V.; Zefirov, N. S.; Makarenko, A. S.; Tanchuk, V. Y.; Prokopenko, V. V. J Comput Aided Mol Des 2005, 19, 453.
20. Gasteiger, J.; Marsili, M. Tetrahedron 1980, 36, 3219.
21. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J. Proteins 2006, 65, 15.