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J Chem Inf Model. 2005 May-Jun;45(3):673-84.

Small molecule shape-fingerprints.

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Department of Chemistry, The University of Sheffield, Sheffield S3 7HF, England.


The optimal overlap between two molecular structures is a useful measure of shape similarity. However, it usually requires significant computation. This work describes the design of shape-fingerprints: binary bit strings that encode molecular shape. Standard measures of similarity between two shape-fingerprints are shown to be an excellent surrogate for similarity based on volume overlap but several orders of magnitude faster to compute. Consequently, shape-fingerprints can be used for clustering of large data sets, evaluating the diversity of compound libraries, as descriptors in SAR and as a prescreen for exact shape comparison against large virtual databases. Our results show that a small set of shapes can be used to build these fingerprints and that this set can be applied universally.


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