An intersection inequality sharper than the tanimoto triangle inequality for efficiently searching large databases

Journal of Chemical Information and Modeling

Volumn 49, Issue 8, 2009, Pages 1866-1870

  Baldi, Pierre ^a   Hirschberg, Daniel S ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL ENGINEERING; CHEMISTRY;

BINARY FINGERPRINTS; FINGERPRINT VECTOR; INTEGER REPRESENTATION; MOLECULAR FINGERPRINT; SIMILARITY MEASURE; SMALL MOLECULES; TANIMOTO DISTANCES; TRIANGLE INEQUALITY;

DATABASE SYSTEMS;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; FACTUAL DATABASE;

ALGORITHMS; DATABASES, FACTUAL; MOLECULAR STRUCTURE;

EID: 69549086567     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci900133j     Document Type: Article

References (13)

1. Burkhard, W.; Keller, R. Some Approaches to Best-Match File Searching. Commun. ACM 1973, 16, 230-236.
2. Shapiro, M. The Choice of Reference Points in Best-Match File Searching. Commun. ACM 1977, 20, 339-343.
3. Shasha, D.; Wang, T.-L. New Techniques for Best-Match Retrieval. ACM Trans. Inf. Syst. 1990, 8, 140-158.
4. Downs, G. M.; Willett, P. Similarity Searching and Clustering of Chemical-Structure Databases Using Molecular Property Data. J. Chem. Inf. Comput. Sci. 1994, 34, 1094-1102.
5. Swamidass, S.; Baldi, P. Bounds and Algorithms for Exact Searches of Chemical Fingerprints in Linear and Sub-Linear Time. J. Chem. Inf. Model. 2007, 47, 302-317.
6. Willett, P.; Barnard, J.; Downs, G. Chemical Similarity Searching. J. Chem. Inf. Comp. Sci. 1998, 38, 983-996.
7. Leach, A. R.; Gillet, V. J. An Introduction to Chemoinformatics; Springer: Dordrecht, The Netherlands, 2005.
8. Chen, J.; Swamidass, S. J.; Dou, Y.; Bruand, J.; Baldi, P. ChemDB: a Public Database of Small Molecules and Related Chemoinformatics Resources. Bioinformatics 2005, 21, 4133-4139.
9. Baldi, P.; Hirschberg, D. S.; Nasr, R. J. Speeding Up Chemical Database Searches Using a Proximity Filter Based on the Logical Exclusive-OR. J. Chem. Inf. Model. 2008, 48, 1367-1378.
10. Spath, H. Cluster Analysis Algorithms; Ellis Horwood: 1980.
11. Lipkus, A. A Proof of the Triangle Inequality for the Tanimoto Distance. J. Math. Chem. 1999, 26, 263-265.
12. (12) Holliday, J. D.; Hu, C. Y.; Willett, P. Grouping of Coefficients for the Calculation of Inter-Molecular Similarity and Dissimilarity Using 2D Fragment Bit-Strings. Comb. Chem. High Throughput Screening 2002, 5, 155-166. (Pubitemid 34475167)
13. Chen, J.; Linstead, E.; Swamidass, S. J.; Wang, D.; Baldi, P. ChemDB Update-Full Text Search and Virtual Chemical Space. Bioinformatics 2007, 23, 2348-2351.