Software news and update AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

Journal of Computational Chemistry

Volumn 31, Issue 2, 2010, Pages 455-461

  Trott, Oleg ^a   Olson, Arthur J ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

AutoDock; Computer aided drug design; Molecular docking; Multithreading; Scoring function; Virtual screening

Indexed keywords

BINDING ENERGY; MOLECULAR MODELING;

AUTODOCK; COMPUTER AIDED DRUG DESIGN; MOLECULAR DOCKING; MULTI-THREADING; SCORING FUNCTIONS; VIRTUAL SCREENING;

SOFTWARE TESTING;

LIGAND; SOLVENT;

ALGORITHM; ARTICLE; AUTOMATION; BINDING SITE; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; HYDROGEN BOND; HYDROPHOBICITY; METHODOLOGY; MOLECULAR DYNAMICS; SENSITIVITY AND SPECIFICITY; THERMODYNAMICS; TIME;

ALGORITHMS; AUTOMATION; BINDING SITES; COMPUTATIONAL BIOLOGY; HYDROGEN BONDING; HYDROPHOBICITY; LIGANDS; MOLECULAR DYNAMICS SIMULATION; SENSITIVITY AND SPECIFICITY; SOFTWARE; SOLVENTS; THERMODYNAMICS; TIME FACTORS;

EID: 76149120388     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: None     Document Type: Article

References (25)

1. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J. Proteins-Struct Funct Bioinformatics 2006, 65, 15.
2. Chang, M. W.; Lindstrom, W.; Olson, A. J.; Belew, R. K. J Chem Inf Model 2007, 47, 1258.
3. Gilson, M. K.; Zhou, H.-X. Annu Re Biophys Biomole Struct 2007, 36, 21.
4. Gilson, M.; Given, J.; Bush, B.; McCammon, J. Biophys J 1997, 72, 1047.
5. Chang, C.-E. A.; Chen, W.; Gilson, M. K. Proc Nat Acad Sci USA 2007, 104, 1534.
6. Morris, G.; Goodsell, D.; Halliday, R.; Huey, R.; Hart, W.; Belew, R.; Olson, A. J Comput Chem 1998, 19, 1639.
7. Vanopdenbosch, N.; Cramer, R.; Giarrusso, F.; J Mol Graph 1985, 3, 110.
8. Wang, R.; Lai, L.; Wang, S. J Comput-Aided Mol Des 2002, 16, 11.
9. Wang, R.; Fang, X.; Lu, Y.; Wang, S. J Med Chem 2004, 47, 2977.
10. Wang, R.; Fang, X.; Lu, Y.; Yang, C.; Wang, S. J Med Chem 2005, 48, 4111.
11. Jain, A. J Comput-Aided Mol Des 1996, 10, 427.
12. Holland, J. H. Adaptation in Natural and Artificial Systems; The University of Michigan Press: Ann Arbor, 1975.
13. Eberhart, R.; Kennedy, J. Proceedings of the Sixth International Symposium on Micro Machine and Human Science; 1995, 39.
14. Kennedy, J.; Eberhart, R. Proc IEEE Int Conf Neural Netw 1995, 4, 1942.
15. Kirkpatrick, S.; Gelatt, C.; Vecchi, M. Science 1983, 220, 671.
16. Baxter, J. J Oper Res Soc 1981, 32, 815.
17. Blum, A. R. C.; Blesa, M.; Sampels, M. Eds. Hybrid Metaheuristics: An Emerging Approach to Optimization; Springer-Verlag, Berlin, Heidelberg, 2008.
18. Abagyan, R.; Totrov, M.; Kuznetsov, D.; J Comput Chem. 1994, 15, 488.
19. Nocedal, J.; Wright, S. J. Numerical Optimization; Springer Verlag: Berlin, 1999, Springer Series in Operations Research.
20. Stroustrup, B. The Design and Evolution of C++; Addison-Wesley, Reading, MA, 1994.
21. Austern, M. H. Generic Programming and the STL; Addison-Wesley, Reading, MA, 1999.
22. Boost Organization, 2008. Boost C++ Libraries. Available at: http://www.boost.org/.
23. Morris, G.; Huey, R.; Lindstrom, W.; Sanner, M.; Belew, R.; Goodsell, D.; Olson, A. J Comput Chem 2009, 30, 2785.
24. Chang, M. W.; Belew, R. K.; Carroll, K. S.; Olson, A. J.; Goodsell,D. S. J Comput Chem 2008, 29, 1753.
25. Bursulaya, B.; Totrov, M.; Abagyan, R.; Brooks, C. J Comput-Aided Mol Des 2003, 17, 755.