Comparative Molecular Similarity Indices Analysis: CoMSIA

Perspectives in Drug Discovery and Design

Volumn 12, Issue , 1998, Pages 87-104

  Klebe, Gerhard ^a  

^a PHILIPPS UNIVERSITY MARBURG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0542451678     PISSN: 09282866     EISSN: None     Source Type: Journal    
DOI: 10.1023/a:1017025803403     Document Type: Article

References (25)

1. Klebe, G., Structural alignment of molecules, In Kubinyi, H. (Ed.) 3D QSAR in drug design, ESCOM, Leiden, The Netherlands, 1993, pp. 173-199.
2. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, T., The protein data bank: a computer-based archival file for Macromolecular structures, J. Mol. Biol., 112 (1977) 535-542.
3. Meyer, E.F., Botos, I., Scapozza, L. and Zhang, D., Backward binding and other structural surprises, Persp. Drug Discov. Design, 3 (1996) 168-195.
4. Böhm, H.J. and Klebe, G., What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs?, Angew. Chem. Int. Ed. Engl., 35 (1996) 2588-2614.
5. Kearsley, S.K. and Smith, G.M., An alternative method for the alignment of molecular structures: Maximizing electrostatic and steric overlap, Tetrahed. Comput. Meth., 3 (1990) 615-633.
6. Klebe, G., Mietzner, T. and Weber, F., Different approaches toward an automatic alignment of drug molecules: Applications to sterol mimics, thrombin and thermolysin inhibitors, J. Comput.-Aided Mol. Design, 8 (1994) 751-778.
7. Klebe, G., Toward a more efficient handling of conformational flexibility in computer-assisted modeling of drug molecules, Persp. Drug Discov. Design, 3 (1995) 85-105.
8. Klebe, G., Mietzner, W. and Weber, F., Methodological developments and strategies for a fast flexible superposition of drug-size molecules (in preparation).
9. Klebe, G. and Mietzner, T., A fast and efficient method to generate biologically relevant conformations, J. Comput.-Aided Mol. Design, 8 (1994) 583-606.
10. Cramer III, R.D., Patterson, D.E. and Bunce, J.D., Comparative molecular field analysis (CoMFA): 1. Effect of shape on binding of steroids to carrier proteins, J. Am. Chem. Soc., 110 (1988) 5959-5967.
11. Klebe, G. and Abraham, U., On the prediction of binding properties of drug molecules by comparative molecular field analysis, J. Med. Chem., 36 (1993) 70-80.
12. Kellogg, G.E. and Abraham, D.J., KEY, LOCK, and LOCKSMITH: Complementary hydrophathic map predictions of drug structure from a known receptor-receptor structure from known drugs, J. Mol. Graph., 10 (1992) 212-217.
13. Kellog, G.E., Joshi, G.S. and Abraham, D.J., New tools for modeling and understanding hydrophobicity and hydrophobic interactions, Med. Chem. Res., 1 (1992) 444-453.
14. Goodford, P.J., A computational procedure for determining energetically favorable binding sites on biologically important macromolecules, J. Med. Chem., 28 (1985) 849-857.
15. Thibaut, U., Applications of CoMFA and related 3D QSAR approaches, In Kubinyi, H. (Ed.), 3D QSAR in drug design, ESCOM, Leiden, The Netherlands, 1993, pp. 661-696.
16. SYBYL Molecular Modeling System (Version 5.40), Tripos Ass., 1699 Hanley Road, St. Louis, MO 63144, U.S.A.
17. Cramer, R.D. III, DePriest, S.A., Patterson, D.E. and Hecht, P., The developing practice of comparative molecular field analysis, In Kubinyi, H. (Ed.), 3D QSAR in drug design, ESCOM, Leiden, The Netherlands, 1993, pp. 443-485.
18. Folkers, G., Merz, A. and Rognan, D., CoMFA: Scope and limitations, In Kubinyi, H. (Ed.) 3D QSAR in drug design, ESCOM, Leiden, The Netherlands, 1993, pp. 583-618.
19. Klebe, G., Abraham, U. and Mietzner, T., Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity, J. Med. Chem., 37 (1994) 4130-4146.
20. Stahle, L. and Wold, S., Multivariate data analysis and experimental design in biomedical research, Prog. Med. Chem., 25 (1988) 292-334.
21. Klebe, G. and Abraham, U., results obtained with proprietory datasets.
22. Good, A.C., So, S.-S. and Richards, W.G., Structure-activity relationships from molecular similarity matrices, J. Med. Chem., 36 (1993) 433-438.
23. DePriest, S.A., Mayer, D., Naylor, C.B., Marshall, G.R., 3D QSAR of angiotensin-converting enzyme and thermolysin inhibitors: A comparison of CoMFA models based on deduced and experimentally determined active site geometries, J. Am. Chem. Soc., 115 (1993) 5372-5384.
24. Matthews, B.W., Structural basis of the action of thermolysin and related zinc peptidases, Acc. Chem. Res., 21 (1988) 33-340.
25. Klebe, G. and Abraham, A. Comparative Molecular Similarity Index Analysis (CoMSIA) to study hydrogen bonding properties and to score combinatorial libraries (submitted).