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Comb Chem High Throughput Screen. 2002 Mar;5(2):155-66.

Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings.

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Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, S10 2TN, UK.


This paper compares 22 different similarity coefficients when they are used for searching databases of 2D fragment bit-strings. Experiments with the National Cancer Institute s AIDS and IDAlert databases show that the coefficients fall into several well-marked clusters, in which the members of a cluster will produce comparable rankings of a set of molecules. These clusters provide a basis for selecting combinations of coefficients for use in data fusion experiments. The results of these experiments provide a simple way of increasing the effectiveness of fragment-based similarity searching systems.

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