An efficient molecular docking using conformational space annealing

Journal of Computational Chemistry

Volumn 26, Issue 1, 2005, Pages 78-87

  Lee, Kyoungrim ^a   Czaplewski, Cezary ^b   Kim, Seung Yeon ^a   Lee, Jooyoung ^a  

^a Korea Institute for Advanced Study   (South Korea)

^b UNIVERSITY OF GDA SK   (Poland)

Author keywords

Conformational space annealing; Global optimization; Molecular docking; Monte Carlo with minimization; Receptor ligand complex

Indexed keywords

ANNEALING; COMPUTER SIMULATION; GENETIC ALGORITHMS; GLOBAL OPTIMIZATION; MONTE CARLO METHODS; PROBLEM SOLVING;

CONFORMATIONAL SPACE ANNEALING (CSA); MOLECULAR DOCKING; MONTE CARLO WITH MINIMIZATION; RECEPTOR-LIGAND COMPLEX;

DOCKING;

LIGAND; PROTEIN;

ALGORITHM; ARTICLE; BINDING COMPETITION; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; METHODOLOGY; MONTE CARLO METHOD; PHYSIOLOGY; PROTEIN DATABASE; STATISTICS;

ALGORITHMS; BINDING, COMPETITIVE; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, PROTEIN; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MONTE CARLO METHOD; PROTEINS;

EID: 11144254064     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.20147     Document Type: Article

References (42)

1. Kuntz, I. D. Science 1992, 257, 1078.
2. Blaney, J. M.; Dixon, J. S. Perspect Drug Discov Design 1993, 1, 301.
3. Kuntz, I. D.; Meng, E. C.; Shoichet, B. K. Acc Chem Res 1994, 27, 117.
4. Torsset, J.; Scheraga, H. J. J Comput Chem 1999, 20, 244.
5. Torsset, J.; Scheraga, H. J. J Comput Chem 1999, 20, 412.
6. Apostolakis, J.; Pluckthun, A.; Caflisch, A. J Comput Chem 1998, 19, 21.
7. Jones, G.; Willet, P.; Glen, R. C.; Leach, A. R.; Taylor, R. J Mol Biol 1997, 267, 727.
8. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W.; Belew, R. K.; Olson, A. J. J Comput Chem 1998, 19, 1639.
9. Taylor, R. D.; Jewsbury, P. J.; Essex, J. W. J Comput Aid Mol Des 2002, 16, 151.
10. Taylor, J. S.; Burnett, R. M. Proteins 2000, 41, 173.
11. Abagyan, R.; Totrov, M.; Kuznetsov, D. J Comput Chem 1994, 15, 488.
12. Goodsell, D. S.; Olson, A. J. Proteins 1990, 8, 195.
13. Morris, G. M.; Goodsell, D. S.; Huey, R.; Olson, A. J. J Comput Aid Mol Des 1996, 10, 293.
14. Mongoni, R.; Roccatano, D.; Di Nola, A. Proteins 1999, 35, 153.
15. Nakajima, N.; Higo, J.; Kidera, A.; Nakamura, H. Chem Phys Lett 1992, 278, 297.
16. Lee, J.; Scheraga, H. A.; Rackovsky, S. J Comput Chem 1997, 18, 1222.
17. Lee, J.; Scheraga, H. A. Int J Quantum Chem 1999, 75, 255.
18. Kim, S.-Y.; Lee, S. J.; Lee, J. J Chem Phys 2003, 119, 10274.
19. Lee, J.; Lee, I. H.; Lee, J. Phys Rev Lett 2003, 91, 080201.
20. Lee, J.; Liwo, A.; Ripoll, D. R.; Pillardy, J.; Scheraga, H. A. Proteins Suppl 1999, 3, 204.
21. Lee, J.; Liwo, A.; Ripoll, D. R.; Pillardy, J.; Saunders, J. A.; Gibson, K. D.; Scheraga, H. A. Int J Quantum Chem 2000, 77, 90.
22. Lee, J.; Kim, S.-Y.; Joo, K.; Kim, I.; Lee, J. Proteins 2004, 56, 704.
23. Saunders, J. A.; Scheraga, H. A. Biopolymers 2003, 68, 300.
24. Saunders, J. A.; Scheraga, H. A. Biopolymers 2003, 68, 318.
25. Nayeem, A.; Vila, J.; Scheraga, H. A. J Comput Chem 1991, 12, 594.
26. Trosset, J. Y.; Scheraga, H. A. Proc Natl Acad Sci USA 1998, 95, 8011.
27. Pillardy, J.; Czaplewski, C.; Wedemeyer, W. J.; Scheraga, H. A. Helv Chim Acta 2000, 83, 2214.
28. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M., Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179.
29. Davidon, W. C. Math Program 1975, 9, 1.
30. Shanno, D. F.; Phua, K.-H. J Optimiz Theory App 1978, 25, 507.
31. Bernstein, F. C.; Koetzle, T. F.; Williams, G. J. B.; Meyer, E. F., Jr.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. J Mol Biol 1977, 112, 535.
32. Abola, E. E.; Bernstein, F. C.; Bryant, S. H.; Koetzle, T. F.; Weng, J. In Crystallographic Databases-Information Content, Software Systems, Scientific Applications; Allen, F. H.; Bergerhoff, G.; Sievers, R., Eds.; Data Commission of the International Union of Crystallography: Bonn/Cambridge/Chester, 1987, p. 107.
33. Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M. S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S. J.; Windus, T. L.; Dupuis, M.; Montgomery, J. A. J Comput Chem 1993, 14, 1347.
34. Hariharan, P. C.; Pople, J. A. Chem Phys Lett 1972, 66, 217.
35. Bayly, C. I.; Cieplak, P.; Cornell, W.; Kollman, P. A. J Phys Chem 1993, 97, 10269.
36. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollman, P. A. J Am Chem Soc 1993, 115, 9620.
37. Cieplak, P.; Cornell, W. D.; Bayly, C.; Kollman, P. A. J Comput Chem 1995, 16, 1357.
38. Marquart, M.; Walter, J.; Deisenhofer, J.; Bode, W.; Huber, R. Acta Crystallogr Sect B 1983, 39, 480.
39. Ealick, S. E.; Babu, Y. S.; Bugg, C. E.; Erion, M. D.; Guida, W. C.; Montgomery, J. A.; Secrist, J. A., III. Proc Natl Acad Sci USA 1991, 88, 11540.
40. Gilson, M. K.; Sharp, K. A.; Honig, B. J Comput Chem 1988, 9, 327.
41. Honig, B.; Nicholls, A. Science 1995, 268, 1144.
42. Zou, X.; Sun, Y.; Kuntz, I. D. J Am Chem Soc 1999, 121, 8033.