LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites

Journal of Molecular Graphics and Modelling

Volumn 21, Issue 4, 2003, Pages 289-307

  Venkatachalam, C M ^a   Jiang, X ^a   Oldfield, T ^a   Waldman, M ^a  

^a ACCELRYS INC   (United States)

Author keywords

Active site detection; High throughput docking tools; Ligand docking; LigandFit; Protein ligand complexes

Indexed keywords

ALGORITHMS; ERRORS; INTERPOLATION; MONTE CARLO METHODS; X RAY ANALYSIS;

LIGANDS;

PROTEINS;

LIGAND; RECEPTOR PROTEIN; THYMIDINE KINASE;

ALGORITHM; ANALYTIC METHOD; ANALYTICAL ERROR; ARTICLE; BINDING SITE; LIGANDFIT; MATHEMATICAL ANALYSIS; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN INTERACTION; SCORING SYSTEM; SCREENING TEST; X RAY ANALYSIS;

ALGORITHMS; BINDING SITES; COMPUTER SIMULATION; LIGANDS; MATHEMATICS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOFTWARE;

EID: 0037212102     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1093-3263(02)00164-X     Document Type: Article

References (55)

1. A. Krammer, P.D. Kirchhoff, J. Jiang, C.M. Venkatachalam, M. Waldman, LIGSCORE: A New Scoring Function to Evaluate and Prioritize Ligands Docked to Protein Active Sites (in preparation patent pending).
2. Pattabhiraman N., Levitt M., Ferrin T.E., Langridge R. Computer graphics in real-time docking with energy calculation and minimization. J. Comp. Chem. 6(5):1985;432-436.
3. DesJarlais R.L., Sheridan R.P., Dixon J.S., Kuntz I.D., Venkataraghavan R. Docking flexible ligands to macromolecular receptors by molecular shape. J. Med. Chem. 29(11):1986;2149-2153.
4. DesJarlais R.L., Sheridan R.P., Seibel G.L., Dixon J.S., Kuntz I.D., Venkataraghavan R. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. J. Med. Chem. 31(4):1988;722-729.
5. Meng E.C., Shoichet B.K., Kuntz I.D. Automated docking with grid-based energy evaluations. J. Comp. Chem. 13(4):1992;505-524.
6. Bacon D.J., Moult J. Docking by least-squares fitting of molecular surface patterns. J. Mol. Biol. 225(3):1992;849-858.
7. Sudarsanam S., Virca G.D., March C.J., Srinivasan S. An approach to computer-aided inhibitor design: application to cathepsin L. J. Comput. Aided Mol. Des. 6(3):1992;223-233.
8. DesJarlais R.L., Dixon J.S. A shape- and chemistry-based docking method and its use in the design of HIV-1 protease inhibitors. J. Comput. Aided Mol. Des. 8(3):1994;231-242.
9. Luty B.A., Wasserman Z.R., Stouten P.F.W., Hodge C.N. A molecular mechanics/grid method for evaluation of ligand-receptor interactions. J. Comp. Chem. 16(4):1995;454-464.
10. Oshiro C.M., Kuntz I.D., Dixon J.S. Flexible ligand docking using a genetic algorithm. J. Comput. Aided Mol. Des. 9(2):1995;113-130.
11. Goodsell D.S., Morris G.M., Olson A.J. Automated docking of flexible ligands: applications of AutoDock. J. Mol. Recog. 9(1):1996;1-5.
12. Gschwend D.A., Kuntz I.D. Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal. J. Comput. Aided Mol. Des. 10(2):1996;123-132.
13. Morris G.M., Goodsell D.S., Huey R., Olson A.J. Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. J. Comput. Aided Mol. Des. 10(4):1996;293-304.
14. Rarey M., Kramer B., Lengauer T., Klebe G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 261:1996;470-489.
15. Welch W., Ruppert J., Jain A.N. Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chem. Biol. 3(6):1996;449-462.
16. 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. 267:1997;727-748.
17. Hahn M. Three-dimensional shape-based searching of conformationally flexible compounds. J. Chem. Inf. Comput. Sci. 7(1):1997;80-86.
18. Sun Y., Ewing T.J., Skillman A.G., Kuntz I.D. CombiDOCK: structure-based combinatorial docking and library design. J. Comput. Aided Mol. Des. 12(6):1998;597-604.
19. Trosset J.-Y., Scheraga H.A. Reaching the global minimum in docking simulations: a Monte Carlo energy minimization approach using Bezier splines. Proc. Natl. Acad. Sci. U.S.A. 95:1998;8011-8015.
20. Liu M., Wang S. MCDOCK: a Monte Carlo simulation approach to the molecular docking problem. J. Comput. Aided Mol. Des. 13(5):1999;435-451.
21. Makino S., Ewing T.J., Kuntz I.D. DREAM++: flexible docking program for virtual combinatorial libraries. J. Comput. Aided Mol. Des. 13(5):1999;513-532.
22. Wang J., Kollman P.A., Kuntz I.D. Flexible ligand docking: a multistep strategy approach. Proteins. 36(1):1999;1-19.
23. Cosgrove D.A., Bayada D.M., Johnson A.P. A novel method of aligning molecules by local surface shape similarity. J. Comput. Aided Mol. Des. 14(6):2000;573-591.
24. Fradera X., Knegtel R.M.A., Mestres J. Similarity-driven flexible ligand docking. Proteins. 40:2000;623-636.
25. Goldman B.B., Wipke W.T. QSD quadratic shape descriptors. 2. Molecular docking using quadratic shape descriptors (QSDock). Proteins. 38(1):2000;79-94.
26. David L., Luo R., Gilson M.K. Ligand-receptor docking with the mining minima optimizer. J. Comput. Aided Mol. Des. 15(2):2001;157-171.
27. Diller D.J., Merz K.M.J. High throughput docking for library design and library prioritization. Proteins. 43:2001;113-124.
28. 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. 15(5):2001;411-428.
29. Kirchhoff P.D., Brown R., Kahn S., Waldman M., Venkatachalam C.M. Application of structure-based focusing to the estrogen receptor. J. Comp. Chem. 22(10):2001;993-1003.
30. Kuntz I.D., Blaney J.M., Oatley S.J., Langridge R., Ferrin T.E. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161(2):1982;269-288.
31. Oldfield T.J. A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solvent. Acta Cryst. D57:2001;82-94.
32. Oldfield T.J. X-LIGAND: an application for the automated addition of flexible ligands into electron density. Acta Cryst. D57:2001;696-705.
33. J.D. Foley, A. Van Dam, Fundamentals of Interactive Computer Graphics, Addison-Wesley, Reading, MA, 1982, p. 664.
34. D.F. Rogers, Procedural Elements for Computer Graphics, McGraw-Hill, New York, 1985, p. 433.
35. R. Fletcher, Practical methods of optimization, in: Unconstrained Optimization, vol. 1, 1980, Wiley, New York.
36. L.E. Scales, Introduction to Non-Linear Optimization, Springer-Verlag, New York, 1985, p. 243.
37. U. Dinur, A.T. Hagler, New approaches to empirical force fields, in: Reviews of Computational Chemistry, 1991 (Chapter 4).
38. Maple J.R., Dinur U., Hagler A.T. Proc. Natl. Acad. Sci. U.S.A. 85:1988;5350-5354.
39. Peng Z., Ewig C.S., Hwang M.-J., Waldman M., Hagler A.T. Derivation of class II force fields. 4. van der Waals parameters of alkali metal cations and halide anions. J. Phys. Chem. A. 101(39):1997;7243-7252.
40. Ewig C.S., Berry R., Dinur U., Hill J.-R., Hwang M.-J., Li H., Liang C., Maple J., Peng Z., Stockfisch T.P., Thacher T.S., Yan L., Ni X., Hagler A.T. Derivation of class II force fields. VIII. derivation of a general quantum mechanical force field for organic compounds. J. Comp. Chem. 22(15):2001;1782-1800.
41. Mayo S.L., Olafson B.D., Goddard W.A.I. DREIDING: a generic force field for molecular simulations. J. Phys. Chem. 94:1990;8897-8909.
42. Oberlin D.J., Scheraga H.A. B-Spline method for energy minimization in grid-based molecular mechanics calculations. J. Comp. Chem. 19(1):1998;71-85.
43. Levitt M. Protein folding by restrained energy minimization and molecular dynamics. J. Mol. Biol. 170(3):1983;723-764.
44. Bohm H.J. Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or three-dimensional database search programs. J. Comput. Aided Mol. Des. 12(4):1998;309-323.
45. Gehlhaar D.K., Verkhivker G.M., Rejto P.A., Sherman C.J., Fogel D.B., Fogel L.J., Freer S.T. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. Chem. Biol. 2:1995;317-324.
46. Verkhivker G.M., Bouzida D., Gehlhaar D.K., Rejto P.A., Arthurs S., Colson A.B., Freer S.T., Larson V., Luty B.A., Marrone T., Rose P.W. Deciphering common failures in molecular docking of ligand-protein complexes. J. Comput. Aided. Mol. Des. 14(8):2000;731-751.
47. Muegge I., Martin Y.C. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J. Med. Chem. 42(5):1999;791-804.
48. Rogers D., Hopfinger A.J. Application of genetic function approximation to quantitative structure-activity relationships and quantitative structure property relationships. J. Chem. Inf. Comput. Sci. 34(4):1994;854-866.
49. D. Rogers, Evolutionary statistics: Using a genetic algorithm and model reduction to isolate alternate statistical hypothses of experimental data, in: Proceedings of the 7th International Conference on Genetic Algorithm, East Lansing, MI, 1997.
50. Bissantz C., Folkers G., Rognan D. Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J. Med. Chem. 43(25):2000;4759-4767.
51. J. Gasteiger, M. Marsili, A new model for calculating atomic charges in molecules, Tetrahedron Lett. (1978) 3181-3184.
52. D.K. Gehlhaar, D. Bouzida, P.A. Rejto, Reduced dimensionality in ligand-protein structure prediction: Covalent inhibitors of serine proteases and design of site-directed combinatorial libraries, in: A.L. Parrill, M.R. Reddy (Eds.), Rational Drug Design: Novel Methodology and Practical Applications, vol. 719, American Chemical Society, Washington, DC, 1999, pp. 292-311.
53. X. Jiang, unpublished work.
54. Charifson P.S., Corkery J.J., Murcko M.A., Walters W.P. Consensus scoring: a method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J. Med. Chem. 42:1999;5100-5109.
55. Clark R.D., Strizhev A., Leonard J.M., Blake J.F., Matthew J.B. Consensus scoring for ligand/protein interactions. J. Mol. Graphics Modell. 20:2002;281-295.