Conformational sampling with stochastic proximity embedding and self-organizing superimposition: Establishing reasonable parameters for their practical use

Journal of Chemical Information and Modeling

Volumn 49, Issue 12, 2009, Pages 2786-2800

  Tresadern, Gary ^a,b   Agrafiotis, Dimitris K ^b  

^a JOHNSON AND JOHNSON   (United States)

^b JOHNSON AND JOHNSON PHARMACEUTICAL RESEARCH AND DEVELOPMENT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EMBEDDINGS; STOCHASTIC SYSTEMS;

CONFORMATIONAL SAMPLINGS; CONFORMATIONAL SEARCH; PARAMETER SETTING; PRACTICAL USE; RESIDUAL STRAINS; SEARCH PROTOCOLS; VALIDATION STUDY; VIRTUAL SCREENING;

CONFORMATIONS;

LIGAND; PROTEIN;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DRUG SCREENING; METABOLISM; METHODOLOGY; REPRODUCIBILITY; STANDARD; STATISTICS; THERMODYNAMICS; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; CRYSTALLOGRAPHY, X-RAY; DRUG EVALUATION, PRECLINICAL; LIGANDS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; PROTEINS; REFERENCE STANDARDS; REPRODUCIBILITY OF RESULTS; STOCHASTIC PROCESSES; THERMODYNAMICS;

EID: 73349120955     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci9001926     Document Type: Article

References (38)

1. Stockwell, G. R.; Thornton, J. M. Conformational diversity of ligands bound to protein. J. Mol, Biol. 2006, 356, 928-944.
2. Leach, A. R. Survey of methods for searching the conformational space of small and medium-sized molecules. In Reviews in Computational Chemistry: Lipkowitz, K. B., Boyd, D. B., Eds.; VCH: New York, 1991.
3. Lipton, M.; Still, W. C. The multiple minimum problem in molecular modeling. Tree searching internal coordinate conformational space. J. Comput, Chem. 1988, 9, 343.
4. Bruccoleri, R. E.; Karplus, M. Chain closure with bond angle variations. Macromolecules 1985, 18, 2767.
5. Bruccoleri, R. E.; Karplus, M. Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers 1987, 26, 137.
6. Go, N.; Scheraga, H. A. Ring closure and local conformational deformations of chain molecules. Macromolecules 1970, 3, 178.
7. Saunders, M. Stochastic explorations of molecular mechanics energy surfaces. Hunting for the global minimum. J. Am. Chem. Soc. 1987, 109, 3150.
8. Ferguson, D. M.; Raber, D. J. A new approach to probing conformational space with molecular mechanics: random incremental pulse search. J. Am. Chem. Soc.1989, 111, 4371.
9. Chang, G.; Guida, W. C.; Still, W. C. An internal-coordinate Monte Carlo method for searching conformational space. J. Am. Chem. Soc. 1989, 111, 4379-4386.
10. Li, Z.; Scheraga, H. A. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 6611-6615.
11. Jorgensen, W. L.; Tirado-Rives, J. Monte Carlo vs molecular dynamics for conformational sampling. J. Phvs. Chem. 1996, 100, 14508-14513. (Pubitemid 126796548)
12. Bostrom, J. Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools. J. Comput,-Aided Mol. Des. 2001, 15, 1137-1152.
13. Bostrom, J.; Greenwood, J. R.; Gottfries J. R.; Gottfries, J. Assessing the performance of OMEGA with respect to retrieving bioactive conformations. J. Mol. Graphics Modell. 2003, 21, 449-462. (Pubitemid 36120775)
14. Perola, E.; Charifson, P. S. Conformational analysis of drug-like molecules bound to proteins: An extensive study of ligand reorganization upon binding. J. Med. Chem. 2004, 47, 2499-2510.
15. Nicklaus, M. C;. Wang, S.; Driscoll, J. S.; Milne, G. W. A. Conformational changes of small molecules binding to proteins. Bioorg. Med. Chem. 1995, 3, 411-428.
16. Vieth, M.; Hirst, J. D.; Brooks, C. L. Do active site conformations of small ligands correspond to low free-energy solution structures. J. Comput.-Aided Mol. Des. 1998, 12, 563-572.
17. Kirchmair, J.; Laggner, C.; Wolber, G.; Langer, T. Comparative analysis of protein-bound ligand conformations with respect to Catalyst's conformational space subsampling algorithms. J. Chem. Inf. Model. 2005, 45, 422-430.
18. Tirado-Rives, J.; Jorgensen, W. L. Contribution of conformation focusing to the uncertainty in predicting free energies for proteinligand binding. J. Med. Chem. 2006, 49, 5880-5884.
19. Diller, D. J.; Merz, K. M. Can we separate active from inactive conformations. J. Comput.-Aided Mol. Des. 2002, 16, 105-112.
20. Crippen, G. M. Rapid calculation of coordinates from distance matrices. J. Cmput Phys. 1978, 26, 449-452.
21. Spellmeyer, D. C.; Wong, A. K.; Bower, M. J.; Blaney, J. M. Conformational analysis using distance geometry methods. J. Mol. Graphics Modell. 1997, 15, 18.
22. Agrafiotis, D. K. Stochastic proximity embedding. J. Comput. Chem. 2003, 24, 1215-1221.
23. Rassokhin, D. N.; Agrafiotis, D. K. A modified update rule for stochastic proximity embedding. J. Mol. Graphics Modell. 2003, 22, 133-140.
24. Xu, H.; Izrailev, S.; Agrafiotis, D. K. Conformational sampling by self-organization. J. Chem. Inf. Comput. Sci. 2003, 43, 1186-1191.
25. Zhu, F.; Agrafiotis, D. K. Self-organizing superimposition algorithm for conformational sampling. J. Comput. Chem. 2007, 28, 1234-1239.
26. Izrailev, S.; Zhu, F.; Agrafiotis, D. K. A distance geometry heuristic for expanding the range of geometries sampled, during conformational search. J. Comput. Chem. 2006, 27, 1962-1969.
27. Agrafiotis, D. K.; Xu, H. A self-organizing principle for learning nonlinear manifolds. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 1586915872.
28. Agrafiotis, D. K.; Gibbs, A.; Zhu, F.; Izrailev, S.; Martin, E. Conformational boosting. Aust. J. Chem. 2006, 59, 874-878.
29. Agrafiotis, D. K.; Gibbs, A. C.; Zhu, F.; Izrailev, S.; Martin, E. Conformational sampling of bioactive molecules: A comparative study. J. Chem. Inf. Model. 2007, 47, 1067-1086. (Pubitemid 46973722)
30. Agrafiotis, D. K.; Bandyopadhyay, D.; Carta, G.; Knox, A. J.; Lloyd, D. G. On the effects of permuted input on conformational sampling of drug-like molecules: an evaluation of stochastic proximity embedding. Chem. Biol. Drug Des. 2007, 70, 123-133.
31. Chen, I. J.; Foloppe, N. Conformational sampling of druglike molecules with MOE and Catalyst: Implications for pharmacophore modeling and virtual screening. J. Chem. Inf. Model. 2008, 48, 1773-1791.
32. O'Shea, R.; Moser, H. E. Physicochemical properties of antibacterial compounds: Implications for drug discovery. J. Med. Chem. 2008, 51, 2871-2878.
33. Payne, D. J.; Gwynn, M. N.; Holmes, D. J.; Pompliano, D. L. Drugs for bad bugs: confronting the challenges of antibacterial discovery. Nat. Rev. Drug Discovery 2007, 6, 29-40.
34. Pu, L.; Agrafiotis, D. K.; Theobald, D. L. Fast determination of the optimal rotational matrix for weighted superpositions. J. Comput. Chem., in press.
35. Onufriev, A; Bashford, D.; Case, D. A. Modification of the generalized Born model suitable for macromolecules. J. Phys. Chem. B 2000, 104, 3712-3720.
36. Yusuf, D.; Davis, A. M.; Kleywegt, G. J.; Schmitt, S. An alternative method for the evaluation of docking performance: RSR vs RMSD. J. Chem. Inf. Model. 2008, 48, 1411-1422.
37. Martin, E. J.; Hoeffel, T. J. Oriented substituent pharmacophore property space (OSPPREYS): A substituent-based calculation that describes combinatorial library products better than the corresponding product-based calculation. J. Mol. Graphics Modell. 2000, 18, 383403.
38. Bonnet, P.; Agrafiotis, D. K.; Zhu, F.; Martin, E. Conformational analysis of macrocycles: Finding what common search methods miss. J. Chem. Inf. Model., Article ASAP.