Analysis and display of the size dependence of chemical similarity coefficients

Journal of Chemical Information and Computer Sciences

Volumn 43, Issue 3, 2003, Pages 819-828

  Holliday, John D ^a   Salim, Naomie ^a   Whittle, Martin ^a   Willett, Peter ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL SIMILARITY COEFFICIENTS;

CHEMICAL COMPOUNDS; CHEMICAL ELEMENTS; COMPUTATIONAL METHODS; MATHEMATICAL MODELS; MOLECULAR STRUCTURE; MOLECULAR WEIGHT;

MOLECULAR DYNAMICS;

EID: 0037835585     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci034001x     Document Type: Review

References (17)

1. Willett, P.; Barnard, J. M.; Downs, G. M. Chemical Similarity Searching. J. Chem. Inf. Comput. Sci. 1998, 38, 983-996.
2. The Unity software packages are available from Tripos Inc. at URL http://www.tripos.com.
3. Dixon, S. L.; Koehler, R. T. The Hidden Component of Size in Two-Dimensional Fragment Descriptors: Side Effects on Sampling in Bioactive Libraries. J. Med. Chem. 1999, 42, 2887-2900.
4. Lajiness, M. S. Dissimilarity-based Compound Selection Techniques. Persp. Drug Discuss. Design 1997, 7/8, 65-84.
5. Whittle, M.; Willett, P.; Klaffte, W.; van-Noort, P. Evaluation of Similarity Measures for Searching the Dictionary of Natural Products Database. J. Chem. Inf. Comput. Sci. 2003, 43, 449-457.
6. Holliday, J. D.; Hu, C.-Y.; Willett, P. Grouping of Coefficients for the Calculation of Intermolecular Similarity and Dissimilarity Using 2D Fragment Bit-Strings. Combin. Chem. High-Through. Screening 2002, 5, 155-166.
7. Flower, D. R. On the Properties of String-Based Chemical Similarity. J. Chem. Inf. Comput. Sci. 1997, 38, 379-386.
8. Godden, J. W., Xue, L. and 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. The Dictionary of Natural Products database is available from Chapman & Hall/CRC at URL http://www.crcpress.com/
10. The MDDR database is available from MDL Information Systems at URL http://www.mdli.com/dats/pharmdb.html.
11. The AIDS database is available from the NCI/NIH Developmental Therapeutics Programme at URL http://dtp.nci.nih.gov/
12. Press: W. H., Teukolsky, S. A, Vetterling, W. T., Flannery, B. P. Numerical Recipies in C, 2nd ed.; Cambridge University Press: 1994.
13. Hann M. M., Leach, A. R., Harper, G., Molecular complexity and its impact on the probability of finding leads for drug discovery. J. Chem. Inf. Comput. Sci. 2001, 41, 856-864.
14. Oprea, T. J., Current trends in lead discovery: Are we looking for the appropriate properties? J. Comput.-Aided Mol. Des. 2002, 16, 325-334.
15. Fligner, M. A.; Verducci, J. S.; Blower, P. E. A Modification of the Jaccard-Tanimoto Similarity Index for Diverse Selection of Chemical Compounds Using Binary Strings. Technometrics 2002, 44, 110-119.
16. Salim, N. Analysis and Comparison of Molecular Similarity Measures. Thesis submitted to the University of Sheffield, 2002.
17. Sheriden, R. P.; Kearsley, S. K. Why do we Need so Many Chemical Similarity Search Methods? Drug Discov. Today 2002, 17, 903-911.