Ligand-protein docking using a quantum stochastic tunneling optimization method

Journal of Computational Chemistry

Volumn 25, Issue 6, 2004, Pages 858-864

  Mancera, Ricardo L ^a  

^a De Novo Pharmaceuticals Ltd   (United Kingdom)

Author keywords

Binding mode; Drug design; Easy dock; Flexible docking; Ligand protein interactions; Molecular docking; Protein ligand data set; Quantum stochastic tunneling

Indexed keywords

BINDING ENERGY; COMPUTER SIMULATION; DRUG PRODUCTS; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; OPTIMIZATION; PRODUCT DEVELOPMENT; QUANTUM THEORY; RANDOM PROCESSES;

BINDING MODE; DRUG DESIGN; LIGAND-PROTEIN DOCKING; LIGAND-PROTEIN INTERACTIONS; MOLECULAR DOCKING; QUANTUM STOCHASTIC TUNNELING OPTIMIZATION METHOD;

PROTEINS;

LIGAND; PROTEIN;

ALGORITHM; ARTICLE; CHEMISTRY; COMPUTER SIMULATION; DRUG DESIGN; PROTEIN BINDING; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; LIGANDS; PROTEIN BINDING; PROTEINS; THERMODYNAMICS;

EID: 1942454773     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.20022     Document Type: Article

References (25)

1. Glen, R. C.; Allen, S. C. Curr Med Chem 2003, 10, 767-782.
2. Stahl, M.; Schulz-Gasch, T. Ernst Schering Res Found Workshop 2003, 42, 127-151.
3. Taylor, R. D.; Jewsbury, P. J.; Essex, J. W. J Comp-Aided Mol Des 2002, 16, 151-166.
4. Stahl, M.; Rarey, M. J Med Chem 2001, 44, 1035-1042.
5. Verkhivker, G. M.; Bouzida, D.; Gehlhaar, D. K.; Rejto, P. A.; Freer, S. T.; Rose, P. W. Curr Opin Struct Biol 2002, 12, 197-203.
6. Ajay; Murcko, M. A. J Med Chem 1995, 38, 4953-4967.
7. Carlson, H. A. Curr Opin Chem Biol 2002, 6, 1-6.
8. Charifson, P. S.; Corkery, J. J.; Murcko, M. A.; Walters, W. P. J Med Chem 1999, 42, 5100-5109.
9. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. J Mol Biol 1996, 261, 470-489.
10. Gehlhaar, D. K.; Verkhivker, G. M.; Rejto, P. A.; Sherman, C. J.; Fogel, D. B.; Fogel, L. J.; Freer, S. T. Chem Biol 1995, 2, 317-324.
11. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. J Mol Biol 1997, 267, 727-748.
12. McMartin, C.; Bohacek, R. S. J Comp-Aided Mol Des 1997, 11, 333-344.
13. Wang, J.; Dixon, R.; Kollman, P. A. Proteins 1999, 34, 69-81.
14. Morris, G. M.; Goodsell, D. S.; Huey, R.; Olson, A. J. J Comp-Aided Mol Des 1996, 10, 293-304.
15. Merlitz, H; Wenzel, W. Chem Phys Lett 2002, 362, 271-277.
16. Merlitz, H.; Burghardt, B.; Wenzel, W. Chem Phys Lett 2003, 370, 68-73.
17. Todorov, N. P.; Mancera, R. L.; Monthoux, P. H. Chem Phys Lett 2003, 369, 257-263.
18. Hansmann, U. H. E. Eur Phys J B 1999, 12, 607-611.
19. Wenzel, W.; Hamacher, K. Phys Rev Lett 1999, 82, 3003-3007.
20. Feynman, R. P.; Hibbs, A. R. Quantum Mechanics and Path Integrals; McGraw-Hill: New York, 1965.
21. Suzuki, M. Proger Theor Phys 1976, 56, 1454-1469.
22. Pollock, E. L.; Ceperley, D. M. Phys Rev B 1984, 30, 2555-2568.
23. Lee, Y.-H.; Berne, B. J. J Phys Chem A 2000, 104, 86-95.
24. Chandler, D.; Wolynes, P. G. J Chem Phys 1981, 74, 4078-4095.
25. Nissink, J. W. M.; Murray, C.; Hartshorn, M.; Verdonk, M. L.; Cole, J. C.; Taylor, R. Proteins 2002, 49, 457-471.