Domain-based small molecule binding site annotation

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. Description: Using a set of co-crystallized protein-small molecule structures as a starting point, SMID interactions were generated by identifying protein domains that bind to small molecules, using NCBI's Reverse Position Specific BLAST (RPS...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Kevin A. Snyder, Howard J. Feldman, Michel Dumontier, John J. Salama, Christopher W. V. Hogue
• Keywords: BMCBI 2006, Molecule Interactions, Protein, Small Molecule