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Nucleic Acids Research 2006 34(Database Issue):D231-D234; doi:10.1093/nar/gkj062
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Nucleic Acids Research, 2006, Vol. 34, Database issue D231-D234
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

SitesBase: a database for structure-based protein–ligand binding site comparisons

Nicola D. Gold and Richard M. Jackson*

Institute of Molecular and Cellular Biology, University of Leeds Leeds LS2 9JT, UK

*To whom correspondence should be addressed. Tel: +44 113 343 2592; Fax: +44 113 343 3167; Email: r.m.jackson{at}leeds.ac.uk

Received August 15, 2005. Revised October 7, 2005. Accepted October 7, 2005.

There are many components which govern the function of a protein within a cell. Here, we focus on the molecular recognition of small molecules and the prediction of common recognition by similarity between protein–ligand binding sites. SitesBase is an easily accessible database which is simple to use and holds information about structural similarities between known ligand binding sites found in the Protein Data Bank. These similarities are presented to the wider community enabling full analysis of molecular recognition and potentially protein structure–function relationships. SitesBase is accessible at http://www.bioinformatics.leeds.ac.uk/sb.


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