Creating artificial binding pocket boundaries to improve the efficiency of flexible ligand docking

Journal of Chemical Information and Computer Sciences

Volumn 44, Issue 4, 2004, Pages 1412-1422

  Brown, W Michael ^a   Jagt, David L Vander ^b  

^a SANDIA NATIONAL LABORATORIES   (United States)

^b UNIVERSITY OF NEW MEXICO SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTIFICIAL BINDING POCKET BOUNDARIES; BINDING-SITE IDENTIFICATION; LIGAND DOCKING; PERFORMANCE OPTIMIZATION;

ALGORITHMS; ATOMS; BIOCHEMISTRY; DIFFERENTIAL EQUATIONS; DOCKING; ENCAPSULATION; ENTHALPY; MACROMOLECULES; PROTEINS; VOLUME MEASUREMENT;

BINDING ENERGY;

DIHYDROFOLATE REDUCTASE; LACTATE DEHYDROGENASE; LIGAND;

ALGORITHM; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; DRUG DESIGN; METABOLISM; THERMODYNAMICS;

ALGORITHMS; BINDING SITES; COMPUTER SIMULATION; DRUG DESIGN; L-LACTATE DEHYDROGENASE; LIGANDS; MODELS, MOLECULAR; TETRAHYDROFOLATE DEHYDROGENASE; THERMODYNAMICS;

EID: 4043054299     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci049853r     Document Type: Article

References (32)

1. Ewing, T. J.; Makino, S.; Skillman, A. G.; Kuntz, I. D. Dock 4.0: Search Strategies for Automated Molecular Docking of Flexible Molecule Databases. J. Comput.-Aided Mol. Des. 2001, 15, 411-428.
2. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A Fast Flexible Docking Method Using an Incremental Construction Algorithm. J. Mol. Biol. 1996, 261, 470-489.
3. Bohm, H. J. Site-Directed Structure Generation by Fragment-Joining. Perspect. Drug Discovery Des. 1995, 3, 21-33.
4. Clark, D. E.; Frenkel, D.; Levy, S.A.; Li, J.; Murray, C. W.; Robson, B.; Waszkowycz, B.; Westhead, D. R. Pro-Ligand: An Approach to De Novo Molecular Design. 1. Application to the Design of Organic Molecules. J. Comput.-Aided Mol. Des. 1995, 9, 13-32.
5. Trosset, J.; Scheraga, H. ProDock: Software Package for Protein Modeling and Docking. J. Comput. Chem. 1999, 20, 412-427.
6. Pang, Y. P.; Perola, E.; Xu, K.; Prendergast, F. G. EUDOC: A Computer Program for Identification of Drug Interaction Sites in Macromolecules and Drug Leads from Chemical Databases. J. Comput. Chem. 2001, 22, 1750-1771.
7. Luo, Z.; Wang, R.; Lai, L. Rasse: A New Method for Structure-Based Drug Design. J. Chem. Inf. Comput. Sci. 1996, 36, 1287-1194.
8. Budin, N.; Majeux, N.; Tenette-Souaille, C.; Caflisch, A. Structure-Based Ligand Design by a Build-up Approach and Genetic Algorithm Search in Conformational Space. J. Comput. Chem. 2001, 22, 1956-1970.
9. Stahl, M.; Bur, D.; Schneider, G. Mapping of Proteinase Active Sites by Projection of Surface-Derived Correlation Vectors. J. Comput. Chem. 1999, 20, 336-347.
10. Liang, J.; Edelsbrunner, H.; Woodward, C. Anatomy of Protein Pockets and Cavities: Measurement of Binding Site Geometry and Implications for Ligand Design. Protein Sci. 1998, 7, 1884-1897.
11. Kuntz, I.; Blaney, J.; Oatley, S.; Langridge, R.; Ferrin, T. A Geometric Approach to Macromolecule-Ligand Interactions. J. Mol. Biol. 1982, 161, 269-288.
12. Ruppert, J.; Welch, W.; Jain, A. N. Automatic Identification and Representation of Protein Binding Sites for Molecular Docking. Protein Sci. 1997, 6, 524-533.
13. Brady, G. P., Jr.; Stouten, P. F. Fast Prediction and Visualization of Protein Binding Pockets with PASS. J. Comput.-Aided Mol. Des. 2000, 14, 383-401.
14. Kleywegt, G.; Jones, T. Detection, Delineation, Measurement and Display of Cavities in Macromolecular Structures. Acta Crystallogr. Sect. D: Biol. Crystallogr. 1994, 50, 178-185.
15. Levitt, D.; Banaszak, L. Pocket - a Computer-Graphics Method for Identifying and Displaying Protein Cavities and Their Surrounding Amino-Acids. J. Mol. Graphics Modell 1992, 10, 229-234.
16. Hendlich, M.; Rippmann, F.; Barnickel, G. LigSite: Automatic and Efficient Detection of Potential Small Molecule-Binding Sites in Proteins. J. Mol. Graphics Modell. 1997, 15, 359-&.
17. Exner, T.; Keil, M.; Moeckel, G.; Brickmann, J. Identification of Substrate Channels and Protein Cavities. J. Mol. Model. 1998, 4, 340-343.
18. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated Docking Using a Lamarckian Genetic Algorithm and Empirical Binding Free Energy Function. J. Comput. Chem. 1998, 19, 1639-1662.
19. Hetenyi, C.; van der Spoel, D. Efficient Docking of Peptides to Proteins without Prior Knowledge of the Binding Site. Protein Sci. 2002, 11, 1729-1737.
20. Lee, B.; Richards, F. M. The Interpretation of Protein Structures: Estimation of Static Accessibility. J. Mol. Biol. 1971, 55, 379-400.
21. Coxeter, H. Introduction to Geometry, 2nd ed.; Coxeter, H., Ed.; Wiley: New York, 1969; Chapter 19, pp 414-434.
22. Richards, F.M. The Interpretation of Protein Structures: Total Volume, Group Volume Distributions and Packing Density. J. Mol. Biol. 1974, 82, 1-14.
23. De Berg, M.; Van Kreveld, M.; Overman, M.; Otfried, S. In Computational Geometry, 2nd ed.; De Berg, M., Ed.; Springer: New York, 2000; Chapter 2, pp 20-29.
24. Li, A. J.; Nussinov, R. A Set of van der Waals and Coulombic Radii of Protein Atoms for Molecular and Solvent-Accessible Surface Calculation, Packing Evaluation, and Docking. Proteins Struct. Funct. Genet. 1998, 52, 111-127.
25. Hou, T.; Wang, J.; Chen, L.; Xu, X. Automated Docking of Peptides and Proteins by Using a Genetic Algorithm Combined with a Tabu Search. Protein Eng. 1999, 12, 639-647.
26. Oshiro, C.; Kuntz, I.; Dixon, J. Flexible Ligand Docking Using a Genetic Algorithm. J. Comput.-Aided Mol. Des. 1995, 9, 113-130.
27. Jones, G.; Willett, P.; Glen, R.; Leach, A.; Taylor, R. Development and Validation of a Genetic Algorithm for Flexible Docking. J. Mol. Biol. 1997, 267, 727-748.
28. Taylor, J.; Burnett, R. Darwin: A Program for Docking Flexible Molecules. Proteins Struct. Funct. Genet. 2000, 41, 173-191.
29. Yang, J.; Kao, C. Flexible Ligand Docking Using a Robust Evolutionary Algorithm. J. Comput. Chem. 2000, 21, 988-998.
30. Nix, A. E.; Vose, M. D. Modeling Genetic Algorithms with Markov Chains. Ann. Math. Artif. Intell. 1991, 5, 79-88.
31. PyMol Software; DeLano Scientific: San Carlos, CA, 2002.
32. Lorensen, W. E.; Cline, H. E. Marching Cubes: A High Resolution 3D Surface Reconstruction Algorithm. Comput. Graphics 1987, 21, 163-169.