Fast 3D molecular superposition and similarity search in databases of flexible molecules

Journal of Computer-Aided Molecular Design

Volumn 17, Issue 1, 2003, Pages 13-38

  Krämer, Andreas ^a   Horn, Hans W ^a   Rice, Julia E ^a  

^a IBM ALMADEN RESEARCH CENTER   (United States)

Author keywords

Database search; Flexible 3D superposition; Molecular similarity; Molecular superposition; Virtual library screening

Indexed keywords

CONFORMATIONS; DIGITAL LIBRARIES; HYDROGEN BONDS; INFORMATION RETRIEVAL; PATTERN MATCHING; QUERY PROCESSING; SEARCH ENGINES;

DATABASE SEARCHES; FLEXIBLE 3D SUPERPOSITION; FLEXIBLE MOLECULES; LIBRARY SCREENING; MOLECULAR FEATURE; MOLECULAR SIMILARITY; MOLECULAR SUPERPOSITION; SIMILARITY SEARCH; VIRTUAL LIBRARIES; VIRTUAL LIBRARY SCREENING;

MOLECULES;

BENZAMIDE; CARBOXYPEPTIDASE A INHIBITOR; COAT PROTEIN; DIHYDROFOLATE REDUCTASE INHIBITOR; DIHYDROFOLIC ACID; ELASTASE INHIBITOR; ENZYME INHIBITOR; FRUCTOSE BISPHOSPHATE; GUANIDINE; HYDROGEN; IMIDAZOLE; LIGAND; METHOTREXATE DERIVATIVE; PURINE; THERMOLYSIN INHIBITOR; THROMBIN INHIBITOR; UNCLASSIFIED DRUG; VIRUS PROTEIN;

ACCURACY; ALGORITHM; ANALYTIC METHOD; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; DATA BASE; DRUG CONFORMATION; DRUG SCREENING; DRUG STRUCTURE; ELECTRICITY; HYDROGEN BOND; HYDROPHOBICITY; INFORMATION PROCESSING; MICROCOMPUTER; MOLECULAR SIZE; PRIORITY JOURNAL; SAMPLING; STRUCTURE ANALYSIS; TIME; VIRTUAL REALITY;

EID: 0042196198     PISSN: 0920654X     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1024503712135     Document Type: Article

References (36)

1. Matter, H. and Rarey., M., In Jung, G. (Ed.) Combinatorial Organic Chemistry. John Wiley & Sons, New York, NY, 1999.
2. Humblet, C. and Dunbar Jr., J.B., In Venuti, M.C. (Ed.) Annual Reports in Medicinal Chemistry. Vol. 28, Chapter VI. Topics in Drug Design and Discovery. Academic Press, London, 1993, pp. 275-284.
3. Willet, P., J. Mol. Recognition, 8 (1995) 290.
4. Brown, R.D. and Martin, Y.C., J. Chem. Inf. Comput. Sci., 36 (1996) 572.
5. Klebe, G., Mietzner, T., and Weber, F., J. Comput. Aided Mol. Des., 8 (1994) 751.
6. Kearsley, S.K. and Smith, G.M., J. Comput. Aided Mol. Des., 8 (1994) 565.
7. Klebe, G., Mietzner, T., and Weber, F., J. Comput. Aided Mol. Des., 13 (1999) 35.
8. Lemmen, C., and Lengauer, T., J. Comput. Aided Mol. Des., 11 (1997) 357.
9. Lemmen, C., Lengauer, T., and Klebe, G., J. Med. Chem., 41 (1998) 4502.
10. Lemmen, C., Hiller, C., and Lengauer, T., J. Comput. Aided Mol. Des., 12 (1998) 491.
11. Miller, M.D., Sheridan, R.P., and Kearsley, S.K., J. Med. Chem., 42 (1999), 1505.
12. Grant, J.A., Gallardo, M.A., Pickup, B.T., J. Comput. Chem., 17 (1996) 1653.
13. McMartin, C. and Bohacek, R.S., J. Med. Chem., 42 (1999) 1505.
14. Handschuh, S., Wagener, M. and Gasteiger, J., J. Chem. Inf. Comput. Sci., 38 (1998) 220.
15. Lemmen, C., and Lengauer, T., J. Comput. Aided Mol. Des., 14 (2000) 215.
16. Lemmen, C., Zimmermann, M., and Lengauer, T., Perspectives in Drug Discovery and Design, 20 (2000) 43.
17. Kearsley, S.K, J. Comput. Chem., 11 (1990) 1187.
18. Diamond, R., Protein Sci., 1 (1992) 1279.
19. Mestres, J., Maggiora, G.M. and Rohrer, D.C., J. Mol. Graph., 15 (1997) 114.
20. Cosgrove, D.A., Bayada, D.M. and Johnson, A.P., J. Comput. Aided Mol. Des., 14 (2000) 573.
21. Labute, P., William, C., Feher, M., Sourial, E. and Schmidt, J.M., J. Med. Chem. 44 (2001) 1483.
22. Mills, J.E.J., de Esch, I.J.P., Perkins, T.D.J. and Dean, P.M., J. Comput. Aided Mol. Des., 15 (2001) 81.
23. Roberts, G.C.K., Drug Discovery Today, 5 (2000) 230.
24. Pitman, M.C., Huber, W.K., Horn, H., Krämer, A., Rice, J.E. and Swope, W.C., J. Comput. Aided Mol. Des., 15 (2001) 587.
25. Lawton, J., Tudor, M. and Wipke, W.T., In Parrill, A.L. and Reddy, M.R. (Eds.) Rational Drug Design: Novel Methodology and Practical Applications. ACS Symposium Series 719, Oxford University Press, 1999, pp. 239-254.
26. FlexS-77 dataset collected by C. Lemmen, G. Klebe, M. Böhm, first published in [9] (http://www.biosolveit.de)
27. Compounds 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 29, 30, 31, 32, 34, 35, 36, 38, 39, 41, 42, 43, 45, 46, 47, 48, 50, 52, 54, 56, 57, 60, 62, 63, 64, 65, 66 from Crippen, G.M., J. Med. Chem. 23 (1980) 599.
28. The NCI diversity set can be found at http://dtp.nci.nih.gov/docs/3ddatabase/structuralinformation/ structuraldata.html.
29. 0 is an atom center and τ = 1 Å [24].
30. See e.g. in Chartrand, G., Introductory Graph Theory, Dover, 1985.
31. See e.g. in Sedgewick, R.,Algorithms in C++, Addison-Wesley, New York, 1992.
32. Pardalos, P.M., University of Florida, 1997.
33. Clark, M., Cramer III, R.D. and Van Opdenbosch, N., J. Comput. Chem. 10 (1989) 982.
34. Bondi, A., J.Phys.Chem., 68 (1964) 441.
35. Mason, J.S., Morize, I, Menard, P.R., Cheney, D.L., Hulme, C. and Labau-diniere, R.F., J. Med. Chem. 42 (1999) 3251.
36. Eksterowicz, J.E., Evensen, E., Lemmen, C., Brady, G.P., Lanctot, J.K., Bradley, E.K., Saiah, E., Robinson, L.A., Grootenhuis, P.D.J. and Blaney, J.M., J. Mol. Graphics Modelling 20 (2002) 469.