Protein-ligand docking against non-native protein conformers

Journal of Chemical Information and Modeling

Volumn 48, Issue 11, 2008, Pages 2214-2225

  Verdonk, Marcel L ^a   Mortenson, Paul N ^a   Hall, Richard J ^a   Hartshorn, Michael J ^a,b   Murray, Christopher W ^a  

^a ASTEX PHARMACEUTICALS   (United Kingdom)

^b Dotmatics Ltd   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; COMPLEXATION; DROPS; LIGANDS;

BINDING MODES; DRUG TARGETS; NATIVE PROTEINS; PROTEIN CONFORMATION; PROTEIN-LIGAND COMPLEXES; PROTEIN-LIGAND DOCKING; REAL-LIFE APPLICATIONS; SMALL VARIATIONS;

PROTEINS;

LIGAND; PROTEIN;

ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; DRUG DESIGN; DRUG SCREENING; INFORMATION SCIENCE; PROTEIN CONFORMATION; PROTEIN DATABASE; STATISTICS;

BINDING SITES; COMPUTER SIMULATION; DATABASES, PROTEIN; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; INFORMATICS; LIGANDS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 57549102789     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci8002254     Document Type: Article

References (29)

1. Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R.; Ferrin, T. E. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 1982, 161, 269-288.
2. Jones, G.; Willett, P.; Glen, R. C. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J. Mol. Biol. 1995. 245, 43-53.
3. Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727-748.
4. 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. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 2004, 47, 1739-1749.
5. Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R.; Halgren, T. A.; Sanschagrin, P. C.; Mainz, D. T. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem. 2006, 49, 6177-6196.
6. Abagyan, R.; Totrov, M.; Kuznetsov, D. ICM-A new method for protein modeling and design - applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem. 1994, 15, 488-506.
7. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235-242.
8. Hartshorn, M. J.; Verdonk, M. L.; Chessari, G.; Brewerton, S. C.; Mooij, W. T.; Mortenson, P. N.; Murray, C. W. Diverse, high-quality test set for the validation of protein-ligand docking performance. J. Med. Chem. 2007, 50, 726-741.
9. Kroemer, R. T.; Vulpetti, A.; McDonald, J. J.; Rohrer, D. C.; Trosset, J. Y.; Giordanetto, F.; Cotesta, S.; Mcmartin, C.; Kihlen, M.; Stouten, P. F. Assessment of docking poses: interactions-based accuracy classification (IBAC) versus crystal structure deviations. J. Chem. Inf. Comput. Sci. 2004, 44, 871-881.
10. Marcou, G.; Rognan, D. Optimizing fragment and scaffold docking by use of molecular interaction fingerprints. J. Chem. Inf. Model. 2007, 47, 195-207.
11. Baxter, C. A.; Murray, C. W.; Clark, D. E.; Westhead, D. R.; Eldridge, M. D. Flexible docking using Tabu search and an empirical estimate of binding affinity. Proteins 1998, 33, 367-382.
12. Murray, C. W.; Baxter, C. A.; Frenkel, A. D. The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase. J. Comput.-Aided Mol. Des. 1999, 13, 547-562.
13. Birch, L.; Murray, C. W.; Hartshorn, M. J.; Tickle, I. J.; Verdonk, M. L. Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase. J Comput.-Aided Mol. Des 2002, 16, 855-869.
14. Erickson, J. A.; Jalaie, M.; Robertson, D. H.; Lewis, R. A.; Vieth, M. Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy. J. Med. Chem. 2004, 47, 45-55.
15. Wu, G.; Robertson, D. H.; Brooks, C. L.; Vieth, M. Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm. J. Comput. Chem. 2003, 24, 1549-1562.
16. Sutherland, J. J.; Nandigam, R. K.; Erickson, J. A.; Vieth, M. Lessons in molecular recognition. 2. Assessing and improving cross-docking accuracy. J. Chem. Inf. Model. 2007, 47, 2293-2302.
17. Cavasotto, C. N.; Abagyan, R. A. Protein flexibility in ligand docking and virtual screening to protein kinases. J. Mol. Biol. 2004, 337, 209-225.
18. Corbeil, C. R.; Englebienne, P.; Moitessier, N. Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0. J. Chem. Inf. Model. 2007, 47, 435-449.
19. Meiler, J.; Baker, D. ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 2006, 65, 538-548.
20. Nabuurs, S. B.; Wagener, M.; de, V. J. A flexible approach to induced fit docking. J. Med. Chem. 2007, 50, 6507-6518.
21. Sherman, W.; Day, T.; Jacobson, M. P.; Friesner, R. A.; Farid, R. Novel procedure for modeling ligand/receptor induced fit effects. J. Med. Chem. 2006, 49, 534-553.
22. Zhao, Y.; Sanner, M. F. FLIPDock: docking flexible ligands into flexible receptors. Proteins 2007, 68, 726-737.
23. Bottegoni, G.; Kufareva, I.; Totrov, M.; Abagyan, R. A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J. Comput.-Aided Mol. Des 2008, 22, 311-325.
24. Claussen, H.; Buning, C.; Rarey, M.; Lengauer, T. FlexE: Efficient molecular docking considering protein structure variations. J. Mol. Biol. 2001, 308, 377-395.
25. Kearsley, S. K. On the orthogonal transformation used for structural comparisons. Acta. Crystallogr. A 1989, 45, 208-210.
26. Verdonk, M. L.; Cole, J. C.; Hartshorn, M.; Murray, C. W.; Taylor, R. D. Improved protein-ligand docking using GOLD. Proteins 2003, 52, 609-623.
27. Tsai, J.; Taylor, R.; Chothia, C.; Gerstein, M. The packing density in proteins: standard radii and volumes. J. Mol. Biol. 1999, 290, 253-266.
28. Hartshorn, M. J. AstexViewer: a visualisation aid for structure-based drug design. J. Comput.-Aided Mol. Des 2002, 16, 871-881.
29. Nissink, J. W. M.; Murray, C. W.; Hartshorn, M. J.; Verdonk, M. L.; Cole, J. C.; Taylor, R. A new test set for validating predictions of protein-ligand interaction. Proteins 2002, 49, 457-471.