Domain-based small molecule binding site annotation.

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.

Description

Using a set of co-crys

SUBMITTER: Snyder KA 

PROVIDER: S-EPMC1435939 | biostudies-literature | 2006 Mar

REPOSITORIES: biostudies-literature