Distinguishing between natural products and synthetic molecules by descriptor Shannon entropy analysis and binary QSAR calculations

Journal of Chemical Information and Computer Sciences

Volumn 40, Issue 5, 2000, Pages 1245-1252

  Stahura, Florence L ^a   Godden, Jeffrey W ^a   Xue, Ling ^a   Bajorath, Jürgen ^b  

^a ALBANY MOLECULAR RESEARCH INC   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DESIGN; ENTROPY; FACTUAL DATABASE; QUANTITATIVE STRUCTURE ACTIVITY RELATION; THERMODYNAMICS;

ALGORITHMS; DATABASES, FACTUAL; DRUG DESIGN; ENTROPY; MODELS, MOLECULAR; PHARMACEUTICAL PREPARATIONS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 0034268411     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci0003303     Document Type: Article

References (25)

1. Henkel, T.; Brunne, R. M.; Müller, H.; Reichel, F. Statistical investigation into the structural complementarity of natural products and synthetic compounds. Angew. Chem., Int. Ed. Engl. 1999, 38, 643-647.
2. Sadowski, J.; Kubinyi, H. A scoring scheme for discriminating between drugs and nondrugs. J. Med. Chem. 1998, 41, 3325-3329.
3. Ajay; Walters, P.; Murcko, M. A. Can we learn to distinguish between "drug-like" and "nondrug-like" molecules? J. Med. Chem. 1998, 41, 3314-3324.
4. Brown, R. D. Descriptors for diversity analysis. Perspect. Drug Discovery Des. 1997, 7/8, 31-49.
5. Brown, R. D.; Martin, Y. C. The information content of 2D and 3D molecular descriptors relevant to ligand-receptor binding. J. Chem. Inf. Comput. Sci. 1997, 37, 731-740.
6. McGregor, M. J.; Pallai, P. V. Clustering of large databases of compounds: Using MDL "keys" as structural descriptors. J. Chem. Inf. Comput. Sci. 1997, 37, 443-448.
7. Matter, H. Selecting optimally diverse compounds from structure databases: A validation study of two-dimensional and three-dimensional molecular descriptors. J. Med. Chem. 1997, 40, 1219-1229.
8. Matter, H.; Pötter, T. Comparing 3D pharmacophore triplets and 2D fingerprints for selecting diverse compound subsets. J. Chem. Inf. Comput. Sci. 1999, 39, 1211-1225.
9. Xue, L.; Godden, J.; Gao, H.; Bajorath, J. Identification of a preferred set of molecular descriptors for compound classification based on principal component analysis. J. Chem. Inf. Comput. Sci. 1999, 39, 669-704.
10. Shannon, C. E.; Weaver, W. The Mathematical Theory of Communication; University of Illinois Press: Urbana, IL, 1963.
11. Godden, J. W.; Stahura, F. L.; Bajorath, J. Variability of molecular descriptors in compound databases revealed by Shannon entropy calculations. J. Chem. Inf. Comput. Sci. 2000, 40, 796-800.
12. Labute, P. Binary QSAR: A new method for the determination of quantitative structure activity relationships. Pac. Symp. Biocomput. 1999, 7, 444-455.
13. Binary QSAR function is part of the "QuaSAR-Model" module of MOE (Molecular Operating Environment), Chemical Computing Group Inc., 1255 University Street, Montreal, Quebec, Canada, H3B 3X3; described in Labute, P. Binary QSAR: A new technology for HTS and UHTS data analysis; electronic publication: http://www.-chemcomp.com/feature/htsbqsar.htm.
14. Binary QSAR function is part of the "QuaSAR-Model" module of MOE (Molecular Operating Environment), Chemical Computing Group Inc., 1255 University Street, Montreal, Quebec, Canada, H3B 3X3; described in Labute, P. Binary QSAR: A new technology for HTS and UHTS data analysis; electronic publication: http://www.-chemcomp.com/feature/htsbqsar.htm.
15. Gao, H.; Williams, C.; Labute, P.; Bajorath, J. Binary quantitative structure activity relationship (QSAR) analysis of estrogen receptor ligands. J. Chem. Inf. Comput. Sci. 1999, 39, 164-168.
16. Gao H.; Bajorath J. Comparison of binary and 2D QSAR analysis using inhibitors of human carbonic anhydrase II as a test case. Mol. Divers. 1999, 4, 115-130.
17. ACD (Available Chemicals Directory); available from MDL Information Systems Inc.: 14600 Catalina Street, San Leandro, CA 94577.
18. Chapman and Hall, Dictionary of Natural Products, CD-ROM 1999 version; CRC Press LLC: NW Corporate Blvd, Boca Raton, FL 33431.
19. MOE (Molecular Operating Environment), version 1999.05; Chemical Computing Group Inc.: 1255 University Street, Montreal, Quebec, Canada, H3B 3X3.
20. MACCS keys; MDL Information Systems, Inc.: 14600 Catalina Street, San Leandro, CA 94557.
21. Feller, W. An Introduction to Probability Theory and its Applications; Wiley & Sons Inc.: New York, 1950; Vol. 1.
22. Glen, W. G.; Dunn, W. J.; Scott, D. R. Principal component analysis and partial least squares regression. Tetrahedron Comput. Methodol. 1989, 2, 349-376.
23. Kier, L. B. Indexes of molecular shape from chemical graphs. Med. Res. Rev. 1987, 7, 417-440.
24. Petitjean, M. Applications of the radius-diameter diagram to the classification of topological and geometrical shapes of chemical compounds. J. Chem. Inf. Comput. Sci. 1992, 32, 331-337.
25. Gasteiger, J.; Marsili, M. Iterative partial equalization of orbital electronegativity - A rapid access to atomic charges. Tetrahedron 1980, 36, 3219-3228.