Importance of accurate charges in molecular docking: Quantum Mechanical/Molecular Mechanical (QM/MM) approach

Journal of Computational Chemistry

Volumn 26, Issue 9, 2005, Pages 915-931

  Cho, Art E ^a   Guallar, Victor ^a,b   Berne, Bruce J ^a   Friesner, Richard ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b WASHINGTON UNIVERSITY   (United States)

Author keywords

DFT; Lead optimization; Protein docking; QM MM

Indexed keywords

DENSITY FUNCTIONAL THEORY (DFT); LEAD OPTIMIZATION; PROTEIN DOCKING; QUANTUM MECHANICAL/MOLECULAR MECHANICAL (QM/MM) CALCULATIONS;

ALGORITHMS; COMPLEXATION; COMPUTATIONAL METHODS; DRUG PRODUCTS; ELECTRIC CHARGE; ITERATIVE METHODS; MOLECULAR DYNAMICS; OPTIMIZATION;

PROTEINS;

LIGAND; PROTEIN;

ALGORITHM; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ELECTROCHEMISTRY; PROTEIN BINDING; THERMODYNAMICS;

ALGORITHMS; BINDING SITES; ELECTROCHEMISTRY; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEIN BINDING; PROTEINS; THERMODYNAMICS;

EID: 20344403522     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.20222     Document Type: Article

References (32)

1. Lengauer, T.; Rarey, M. Curr Opin Struct Biol 1996, 6, 402.
2. Abagyan, R.; Totrov, M. Curr Opin Chem Biol 2001, 5, 375.
3. Kuntz, I. D. Science 1992, 257, 1078.
4. Kramer, B.; Rarey, M.; Lengauer, T. Proteins: Struct, Funct, Genet 1997, 221.
5. Ewing, T. J. A.; Makino, S.; Skillman, A. G.; Kuntz, I. D. J ComputAided Mol Des 2001, 15, 411.
6. Verdonk, M. L.; Cole, J. C.; Hartshorn, M. J.; Murray, C. W.; Taylor, R. D. Proteins: Struct, Funct, Genet 2003, 52, 609.
7. Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz. D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. J Med Chem 2004, 47, 1739.
8. Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L. J Med Chem 2004, 47, 1750.
9. Jorgensen, W. L.; Maxwell, D. S.; TiradoRives, J. J Am Chem Soc 1996, 118, 11225.
10. Murphy, R. B.; Philipp, D. M.; Friesner, R. A. J Comput Chem 2000, 21, 1442.
11. Murphy, R. B.; Philipp, D. M.; Friesner, R. A. Chem Phys Lett 2000, 321, 113.
12. Philipp, D. M.; Friesner, R. A. J Comput Chem 1999, 20, 1468.
13. GLIDE; Schrödinger, LLC: Portland, OR, 2000.
14. Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. J Comput Aid Mol Des 1997, 11, 425.
15. MAESTRO; Schrödinger, LLC: Portland, OR, 2002.
16. IMPACT; Schrödinger, LLC: Portland, OR, 2000.
17. QSITE; Schrödinger, LLC: Portland, OR, 2000.
18. JAGUAR; Schrödinger, LLC: Portland, OR, 2000.
19. Johnson, B. G.; Gill. P. M. W.; Pople, J. A. J Chem Phys 1993, 98, 5612.
20. Lee, C. T.; Yang, W. T.; Parr, R. G. Phys Rev B 1988, 37, 785.
21. Becke, A. D. J Chem Phys 1993, 98, 1372.
22. Becke, A. D. J Chem Phys 1993, 98, 5648.
23. Curtiss, L. A.; Raghavachari, K.; Redfern, P. C.; Pople, J. A. J Chem Phys 1997, 106, 1063.
24. Bauschlicher, C. W. Chem Phys Lett 1995, 246, 40.
25. GLIDE manual; Schrödinger, LLC: Portland, OR, 2002.
26. Casale, E.; Collyer, C.; Ascenzi, P.; Balliano, G.; Milla, P.; Viola, F.; Fasano, M.; Menegatti, E.; Bolognesi, M. Biophys Chem 1995, 54, 75.
27. Kurinov, I. V.; Harrison, R. W. Nat Struct Biol 1994, 1, 735.
28. Quiocho, F. A.; Phillips, G. N.; Parsons, R. G.; Hogg, R. W. J Mol Biol 1974, 86, 491.
29. Quiocho, F. A.; Vyas, N. K. Nature 1984, 310, 381.
30. Quiocho, F. A.; Wilson, D. K.; Vyas, N. K. Nature 1989, 340, 404.
31. Cho, A. E.; Wendel, J. A.; Vaidehi, N.; Kekenes-Huskey, P. M.; Floriano, W. B.; Maiti, P. K.; Goddard, W. A. III. J Comput Chem 2005, 26, 48.
32. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J Am Chem Soc 1990, 112, 6127.