Chemical Similarity Searching

P, J M Barnard and G M Downs 1998. Chemical Similarity Searching. Journal of Chemical irmation and Computer Science 38 983-996. 

Willett P, Barnard JM, Downs, GM Chemical similarity searching. J Chem Inf Comput Sci 1998 38 983-96. 

Sheridan RP, Kearsley SK. Why do we need so many chemical similarity search methods Drug Discov Today 2002 7 903-11. 

C. Pepperrell, Three-Dimensional Chemical Similarity Searching. Research Studies Press (J. Wiley), Taunton, UK, 1994. 

Willett, P., Barnard, J.M., and Downs, G.M. Chemical similarity searching. 

Maggioea, G.M. and Shanmugasundaeam, V. Molecular similarity measures. In Chemometrics Methods and Protocols, Bajoeath, J. (Ed.). Humana Press, Totowa, NJ, 2003, 1-50. Willett, P., Barnard, J.P., and Downs, G.M. Chemical similarity searching. 

Sheridan RP, Kearsley SK. (2002) Why Do We Need So Many Chemical Similarity Search Methods Drug Discov. Today 7 903-911. 

The relationship between IR and chemical similarity searching is discussed in detail by Edgar et al. (11) who summarize the various effectiveness measures in terms of the 2 x 2 contingency table shown in Table 1. In this table, it is assumed that a search has been carried out resulting in the retrieval of the n nearest neighbors at the top of the ranked output. Assume that these n nearest neighbors include a of the A active molecules in the complete database, which contains a total of N molecules. Then the recall, R, is defined to be the fraction of the active molecules that are retrieved, i.e.,... 

Examples of the use of the G-H score are provided by Giiner and Henry (15) and by Raymond and Willett (16), while Edgar et al. discuss other combined measures that can be used for chemical similarity searching (11). 

The following summarizes three related computational approaches that enable the prediction of target or mechanism of action (MOA) from chemical stmcture chemical similarity searching, data mining/machine learning and bioactivity spectra. 

Willett, P. Chemical similarity searching. Journal of Chemical Information and Computer Science 1998, 38, 983-996. 

Free patent information is provided by the website http //www.freepatentsonline.com/, covering U.S., EP, and PCT patents/applications and Japanese patent abstracts. In addition to the usual text-based searches in various search fields, this site also enables graphically input chemical structure searches to be performed on over 9 million compounds (including prophetic compounds) using exact structure, substructure, or chemical similarity searches. Chemistry searches using SMILES strings or chemical names are also possible. Full patent documents may be viewed in text or PDF format. 

---