Domain-based small molecule binding site annotation |
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Authors: | Kevin A Snyder Howard J Feldman Michel Dumontier John J Salama Christopher WV Hogue |
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Institution: | (1) The Blueprint Initiative, 200 Elm St., Suite 101, Toronto ON, M5T 1K4, Canada;(2) Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa ON, K1S 5B6, Canada;(3) Samuel Lunenfeld Research Institute, Room 1060, Mount Sinai Hospital, 600 University Ave., Toronto, Ontario, M5G 1X5, Canada |
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Abstract: | Background Accurate small molecule binding site information for a protein can facilitate studies in drug docking, drug discovery and
function prediction, but small molecule binding site protein sequence annotation is sparse. The Small Molecule Interaction
Database (SMID), a database of protein domain-small molecule interactions, was created using structural data from the Protein
Data Bank (PDB). More importantly it provides a means to predict small molecule binding sites on proteins with a known or
unknown structure and unlike prior approaches, removes large numbers of false positive hits arising from transitive alignment
errors, non-biologically significant small molecules and crystallographic conditions that overpredict ion binding sites. |
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