Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening

Journal of Medicinal Chemistry

Volumn 47, Issue 7, 2004, Pages 1750-1759

  Halgren, Thomas A ^a   Murphy, Robert B ^a   Friesner, Richard A ^b   Beard, Hege S ^a   Frye, Leah L ^a   Pollard, W Thomas ^a   Banks, Jay L ^a  

^a SCHRÖDINGER INC   (United States)

^b Columbia University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESTROGEN RECEPTOR; LIGAND; PROTEIN; THYMIDINE KINASE;

ARTICLE; BINDING AFFINITY; BIOTECHNOLOGY; COMPUTER PROGRAM; DRUG INDUSTRY; PHYSICAL CHEMISTRY; PROTEIN PROTEIN INTERACTION;

BINDING SITES; DATABASES, FACTUAL; DRUG DESIGN; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; PROTEINS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 1642310340     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm030644s     Document Type: Article

References (26)

1. 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.
2. Schrödinger, L.L.C., New York.
3. Jones, G.; Wilett, P.; Glem, R. C.; Leach, A. R.; Taylor, R. Development and validation of a generic algorithm and an empirical binding free energy function. J. Mol. Biol. 1997, 267, 727-748.
4. Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A. A fast flexible docking method using an incremental construction algorithm. Chem. Biol. 1996, 261, 470-489.
5. Rognan, D. Bioinformatic Group, UMR CNRS, France. Personal communication to T.A.H.
6. Bissantz, C.; Folkers, G.; Rognan, D. Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J. Med. Chem. 2000, 43, 4759-4767.
7. Engh, R. A.; Brandstetter, H.; Sucher, G.; Eichinger, A.; Bauman, U.; Bode, W.; Huber, R.; Poll, T.; Rudolph, R.; van der Saal, W. Enzyme flexibility, solvent, and "weak" interactions characterize thrombin-ligand interactions: implications for drug design. Structure 1996, 4, 1353-1362.
8. von der Saal, W.; Kucznierz, R.; Leinart, H.; Engh, R. A. Derivatives of 4-amino-pyridine as selective thrombin inhibitors. Bioorg. Med. Chem. Lett. 1997, 7, 1283-1288.
9. Pearlman, D. A.; Charifson, P. S. Improved scoring of ligand-protein interactions using OWFEG free energy grids. J. Med. Chem. 2001, 44, 502-511.
10. The geometric mean defines the average enrichment factor as the nth root of the product of the n individual enrichment factors. This definition was further modified by replacing any enrichment factor of less than 1 by 1 and by weighting the contributions such that the composite weight is the same for each receptor type, even when two or three receptor site geometries are used.
11. Charifson, P. S.; Corkery, J. J.; Murcko, M. A.; Walters, W. P. Consensus scoring: A method of obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J. Med. Chem. 1999, 42, 5100-5109.
12. Jain, A. N. Surflex: fully automatic flexible molecular docking using a molecular-similarity-based search engine. J. Med. Chem. 2003, 46, 499-511.
13. Murphy, R. B.; Friesner, R. A.; Halgren, T. A. Unpublished results.
14. Stahl, M.; Rarey, M. Detailed analysis of scoring functions for virtual screening. J. Med. Chem. 2001, 44, 1035-1042.
15. Pargellis, C.; Tong, L.; Churchill, L.; Cirillo, P. F.; Gilmore, T.; Graham, A. G.; Grob, P. M.; Hickey, E. R.; Moss, N.; Pav, S.; Regan, J. Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site. Nat. Struct. Biol. 2002, 9, 268.
16. Whittaker, M.; Floyd, C. D.; Brown, P.; Gearing, A. J. H. Design and therapeutic application of matrix metalloproteinase inhibitors. Chem. Rev. 1999, 99, 2735-2776.
17. Babine, R. E.; Bender, S. L. Molecular recognition of protein-ligand complexes: Applications to drug design. Chem. Rev. 1997, 97, 1359-1472.
18. Bell, I. M.; Gallicchio, S. N.; Abrams, M.; Beese, L. S.; Beshore, D. C. ; Bhimnathwala, H.; Bogusky, M. J.; Buser, C. A.; Culberson, J. C.; Davide, J.; Ellis-Hutchings, M.; Fernandes, C.; Gibbs, J. B.; Graham, S. L.; Hamilton, K. A.; Hartman, G. D.; Heimbrook, D. C.; Homnick, C. F.; Huber, H. E.; Huff, J. R. ; Kassahun, K.; et al. 3-Aminopyrrolidinone Farnesyltransferase inhibitors: design of macrocyclic compounds with improved pharmacokinetics and excellent cell potency. J. Med. Chem. 2002, 45, 2388-2409.
19. Schulz-Gasch, T.; Stahl, M. Binding site characteristics in structure-based virtual screening. Evaluation of current docking tools. J. Mol. Model. 2003, 9, 47-57.
20. Ewing, T. J. A.; Kuntz, I. D. Critical evaluation of search algorithms for automated molecular docking and database screening. J. Comput. Chem. 1997, 18, 1175-1189.
21. Lorber, D. M.; Shoichet, B. K. Flexible ligand docking using conformational ensembles. Protein Sci. 1998, 7, 938-950.
22. Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. Empirical scoring functions. I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J. Comput.-Aided Mol. Des. 1997, 11, 425-445.
23. Shoichet, B. K.; Kuntz, I. D. Matching chemistry and shape in molecular docking. Protein Eng. 1993, 6, 723-732.
24. Muegge, I.; Martin, Y. C. A. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J. Med. Chem. 1999, 42, 791-804.
25. Rognan, D.; Laumoeller, S. L.; Holm, A.; Buus, S.; Tschinke, V. Predicting binding affinities of protein ligands from three-dimensional coordinates: Application to peptide binding to class I major histocompatibility proteins. J. Med. Chem. 1999, 42, 6450-4658.
26. Wang, R.; Liu, L.; Tang, Y. SCORE: a new empirical method for estimating the binding affinity of a protein-ligand complex. J. Mol. Model. 1998, 4, 379-384.