Blind docking method combining search of low-resolution binding sites with ligand pose refinement by molecular dynamics-based global optimization

Journal of Computational Chemistry

Volumn 31, Issue 5, 2010, Pages 1080-1092

  Vorobjev, Yury N ^a  

^a INSTITUTE OF CHEMICAL BIOLOGY AND FUNDAMENTAL MEDICINE   (Russian Federation)

Author keywords

Force field deformation; Global optimization; Ligand docking; Molecular dynamics; Scoring functions

Indexed keywords

ACCURACY ASSESSMENT; AUTODOCK; DOCKING METHODS; FIELD DEFORMATIONS; GLOBAL MINIMA; LIGAND BINDING; LIGAND DOCKING; POSE REFINEMENT; PROTEIN SURFACE; PROTEIN-LIGAND COMPLEXES; PROTEIN-LIGAND INTERACTIONS; SCORE FUNCTION; SCORING FUNCTIONS; TWO-STEP ALGORITHMS;

BINDING ENERGY; BINDING SITES; BIOCHEMISTRY; COMPLEXATION; DEFORMATION; DOCKING; DYNAMICS; GLOBAL OPTIMIZATION; GOLD COMPOUNDS; LIGANDS; SIMULATED ANNEALING;

MOLECULAR DYNAMICS;

LIGAND; PROTEIN;

ARTICLE; BINDING SITE; CHEMISTRY; METABOLISM; MOLECULAR DYNAMICS; PROTEIN BINDING;

BINDING SITES; LIGANDS; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEINS;

EID: 77953039644     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21394     Document Type: Article

References (74)

1. Abagyan, R.; Totrov, M. Curr Opin Chem Biol 2001, 5, 375.
2. Halperin, I.; Ma, B.; Wolfson, H. J.; Nussinov, R. Proteins 2002, 47, 409.
3. Yakunin, A. F.; Yee, A. A.; Savchenko, A.; Edwards, A. M.; Arrowsmith, C. H. Curr Opin Chem Biol 2003, 8, 42.
4. Kim, S. H.; Shin, D. H.; Choi, I. G.; Schulze-Gahmen, U.; Chen, S.; Kim, R. J Struct Funct Genomics 2003, 4, 129.
5. Laskowski, R. A.; Watson, D.; Thornton, J. M. J Struct Funct Genomics 2003, 4, 167.
6. Kitchen, D. B.; Decornez, H.; Furr, J. R.; Bajorath, J. Nat Rev Drug Discovery 2004, 3, 935.
7. Shoichet, B. K. Nature 2004, 432, 862.
8. Kim, R.; Skolnick, J. J Comput Chem 2008, 29, 1316.
9. Mohan, V.; Gibbs, A. C.; Cummings, M. D.; Jaeger, E. P.; Desjarlais, R. L. Curr Pharm Des 2005, 11, 323.
10. Krovat, E. M.; Steindl, T.; Langer, T. Curr Comput Aided Drug Des 2005, 1, 93.
11. Leach, A. R.; Shoichet, B. K.; Peishoff, C. E. J Med Chem 2006, 49, 5851.
12. Warren, G. L.; Andrews, C. W.; Capelli, A. M.; Clarke, B.; Lalonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. J Med Chem 2006, 49, 5912.
13. Gilson, M. K.; Given, J. A.; Bush, B. L.; Mccammon, J. A. Biophys J 1997, 72, 1047.
14. Wu, G.; Robertson, D. H.; Brooks, C. L., III; Vieth, M. J Comput Chem 2003, 24, 1549.
15. Grosdidier, A.; Zoete, V.; Michielin, O. Proteins 2007, 67, 1010.
16. Morris, G. M.; Goodseil, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. J Comput Chem 1998, 19, 1639.
17. Ewing, T. J. A.; Kunz, I. D. J Comput Chem 1997, 18, 1176.
18. Kramer, B.; Rarey, M.; Lengauer, T. Proteins 1999, 37, 228.
19. Jones, G.; Willett, P.; Glen, R. C.: Leach, A. R.; Taylor, R. J Mol Biol 1997, 267, 727.
20. Huey, R.; Morris, G. M.; Olson, A. J.; Goodseil, D. S. J Comput Chem 2007, 28, 1145.
21. Chen, H. M.; Liu, B. F.; Huang, H. L.; Hwang, S. F.; Ho, S. Y. J Comput Chem 2007, 28, 612.
22. Nobeli, I.; Mitchell, J. B. O.; Alex, A.; Thornton, J. M. J Comput Chem 2001, 22, 673.
23. Ruvinsky, A. M. J Comput Chem 2007, 28, 1364.
24. Ma, B.; Kumar, S.; Tsai, C. J.; Nussinov, R. Protein Eng 1999, 12, 713.
25. Miller, D. W.; Dili, K. A. Protein Sci 1997, 6, 2166.
26. Goodford, P. J. J Med Chem 1985, 28, 849.
27. Miranker, A.; Karplus, M. Proteins 1991, 11, 29.
28. Brady, G. P.; Stouten, P. F. J Comput Aidded Mol Des 2000, 14, 383.
29. Silberstein, M.; Dennis, S.; Brown, L., III; Kortvelyesi, T.; Clodfelter, T.; Vajda, S. J Mol Biol 2003, 323, 1095.
30. An, J.; Totrov, M.; Abagyan, R. A. Mol Cell Proteomics 2005, 4, 752.
31. Laurie, A. T.; Jackson, R. M. Bioinformatics 2005, 21, 1908.
32. Glaser, F.; Morris, R. J.; Najmanovich, R. J.; Laskowski, R. A.; Thornton, J. M. Proteins 2006, 62, 479.
33. Nayal, M.; Honig, B. Proteins 2006, 63, 892.
34. Kawabata, T.; Go, N. Proteins 2007, 68, 516.
35. Harris, R.; Olson, A. J.; Goodseil, D. S. Proteins 2008, 70, 1506.
36. Morita, M.; Nakamura, S.; Shimizu, K. Proteins 2008, 73, 468.
37. Frankenstein, Z.; Sperling, J.; Sperling, R.: Eisenstein, M. PLoS ONE 2008, 3, e3594.
38. Tovchigrechko, A.; Vakser, I. A. Nucleic Acid Res 2006, 34, W310.
39. Scheidman-Duhovny, D.; Nussinov, R.; Wolfson, H. J. Proteins 2007, 69, 764.
40. Andrusier, N.; Nussinov, R.; Wolfson, H. J. Proteins 2007, 69, 139.
41. Andrusier, N.; Mashiach, E.; Nussinov, R.; Wolfson, H. J. Proteins 2008, 73, 271.
42. Bliznyuk, A. A.; Gready, J. E. J Comput Aided Mol Des 1998, 12, 325.
43. Bliznyuk, A. A.; Gready, J. E. J Comput Chem 1999, 20, 983.
44. Alonso, H.; Bliznyuk, A. A.; Gready, J. E. Med Res Rev 2006, 26, 531.
45. Vieth, M.; Hirst, J. D.; Kolinski, A.; Brooks, C. L., III. J Comput Chem 1998, 19, 1612.
46. Bursulaya, B. D.; Totrov, M.; Abagyan, R.; Brooks, C. L., III. J Comput Aided Mol Des 2003, 17, 755.
47. Chothia, C. J Mol Biol 1976, 105, 1.
48. Richards, F. M. Annu Rev Biophys Bioeng 1977, 6, 151.
49. Vorobjev, Y. N.; Hermans, J. Biophys J 1997, 73, 722.
50. Vorobjev, Y. N. Mol Biol (Translated from Molekulyarnaya Biologiya Rus) 2005, 39, 777.
51. Schlick, T. Molecular Modeling and Simulations; Springer: New York, 2002; Chapter 12.
52. Lazaridis, T.; Karpius, M. Proteins 1999, 35, 133.
53. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179.
54. Wang, J.; Cieplak, P.; Kollman, P. A. J Comput Chem 2000, 21, 1049.
55. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. J Comput Chem 2004, 25, 1157.
56. Rappe, A. K.; Goddard, W. A., III. J Phys Chem 1991, 95, 3358.
57. Scheraga, H. A.; Lee, J.; Pillardy, J.; Ye, Y. J.; Liwo, A.; Ripoll, D. J Global Optimization 1999, 15, 235.
58. Hummer, G.; Soumpasis, D. M.; Neuman, M. Molec Phys 1992, 77, 769.
59. Tironi, I. G.; Sperb, P.; Smith, P. E.; Vangunsteren, W. F. J Phys Chem 1995, 102, 5451.
60. Walser, R.; Hunenberger, P. H.; Van Gunsteren, W. F. Proteins 2001, 44, 509.
61. Vorobjev, Y. N.; Vila, J.; Scheraga, H. A. J Phys Chem B 2008, 112, 11122.
62. Kortemme, T.; Morozov, A. V.; Baker, D. J Mol Biol 2003, 326, 1239.
63. Park, B. H.; Levitt, M. J Mol Biol 1996, 258, 367.
64. Vorobjev, Y. N.; Almagro, H. C.; Hermans, J. Proteins 1998, 32, 399.
65. Vorobjev, Y. N.; Hermans, J. Protein Sci 2001, 10, 2498.
66. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res 2000, 28, 235.
67. Wojciechowski, M.; Skolnick, J. J Comput Chem 2002, 23, 189.
68. Brylinsky, M.; Skolnick, J. J Comput Chem 2008, 29, 1574.
69. Wroblewska, L.; Skolnick, J. J Comput Chem 2007, 28, 2059.
70. Wroblewska, L.; Jagielska, A.; Skolnick, J. Biophys J 2008, 94, 3227.
71. Stote, R. H.; Karplus, M. Proteins 1995, 23, 12.
72. Koca, J.; Zhan, C. G.; Rittenhouse, R. C.; Orastein, R. L. J Comput Chem 2003, 24, 368.
73. Mackerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseek, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-Mccarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586.
74. Lee, M. S.; Feig, M.; Salsbury, F. R.; Brooks, C. L., III. J Comput Chem 2003, 24, 1348.