Balancing the influence of molecular complexity on fingerprint similarity searching

Journal of Chemical Information and Modeling

Volumn 48, Issue 1, 2008, Pages 75-84

  Wang, Yuan ^a   Bajorath, Jürgen ^a  

^a UNIVERSITY OF BONN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DATABASE SYSTEMS; PATTERN RECOGNITION;

COMPLEX MOLECULES; DATABASE COMPOUNDS; MOLECULAR COMPLEXITY;

MOLECULAR DYNAMICS;

ARTICLE; COMPUTER SIMULATION; FACTUAL DATABASE;

COMPUTER SIMULATION; DATABASES, FACTUAL;

EID: 39449093724     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci700314x     Document Type: Article

References (18)

1. Willett, P. Similarity-based Virtual Screening Using 2D Fingerprints. Drug Discovery Today 2006, 11, 1046-1053.
2. Bajorath, J. Selected Concepts and Investigations in Compound Classification, Molecular Descriptor Analysis, and Virtual Screening. J. Chem. Inf. Comput. Sci. 2001, 41, 233-245.
3. Eckert, H.; Bajorath, J. Molecular Similarity Analysis in Virtual Screening: Foundations, Limitations and Novel Approaches. Drug Discovery Today 2007, 12, 225-233.
4. Willett, P.; Barnard, J. M.; Downs, G. M. Chemical Similarity Searching. J. Chem. Inf. Comput. Sci. 1998, 38, 983-996.
5. Maggiora, G. M.; Shanmugasundaram, V. Molecular Similarity Measures. Methods Mol. Biol. 2004, 275, 1-50.
6. Tversky, A. Features of Similarity. Psychol. Rev. 1977, 84, 327-352.
7. Flower, D. R. On the Properties of Bit String-based Measures of Chemical Similarity. J. Chem. Inf. Comput. Sci. 1998, 38, 379-386.
8. Godden, J. W.; Xue, L.; Bajorath, J. Combinatorial Preferences Affect Molecular Similarity/Diversity Calculations using Binary Fingerprints and Tanimoto Coefficients. J. Chem. Inf. Comput. Sci. 2000, 40, 163-166.
9. Chen, X.; Brown, F. K. Asymmetry of Chemical Similarity. ChemMedChem 2007, 2, 180-182.
10. Wang, Y.; Eckert, H.; Bajorath, J. Apparent Asymmetry in Fingerprint Similarity Searching is a Direct Consequence of Differences in Bit Densities and Molecular Size. ChemMedChem 2007, 2, 1037-1042.
11. Eckert, H.; Bajorath, J. Design and Evaluation of a Novel Class-directed 2D Fingerprint to Search for Structurally Diverse Active Compounds. J. Chem. Inf. Model. 2006, 46, 2515-2526.
12. Fligner, M.; Verducci, J.; Blower, P. A Modification of the JaccardTanimoto Similarity Index for Diverse Selection of Chemical Compounds Using Binary Strings. Technometrics 2002, 44, 110-119.
13. Salim, N.; Holliday, J.; Willet, P. Combination of Fingerprint-Based Similarity Coefficients Using Data Fusion. J. Chem. Inf. Comput. Sci. 2003, 43, 435-442.
14. Lajiness, M. S. Dissimilarity-based Compound Selection Techniques. Perspect. Drug. Discovery Des. 1997, 7/8, 65-84.
15. Molecular Drug Data Report (MDDR), version 2005.2; MDL Elsevier: San Leandro, CA, 2005.
16. The publicly available NCI anti-AIDS database contains structural and activity data for compounds screened by the AIDS antiviral screening program of the National Cancer Institute, 1999. http://dtp.nci.nih.gov/docs/aids/aids_data. html (accessed Feb 2007).
17. MACCS structural keys; MDL Elsevier: San Leandro, CA, 2002.
18. Xue, L.; Godden, J. W.; Stahura, F. L.; Bajorath, J. Design and Evaluation of a Molecular Fingerprint Involving the Transformation of Property Descriptor Values into a Binary Classification Scheme. J. Chem. Inf. Comput. Sci. 2003, 43, 1151-1157.