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Nucleic Acids Research, 2004, Vol. 32, Database issue D240-D244
© 2004 Oxford University Press

SURFACE: a database of protein surface regions for functional annotation

Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni and Manuela Helmer-Citterich*

Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy

*To whom correspondence should be addressed. Tel: +39 06 72594314; Fax: +39 06 2023500; Email: citterich{at}uniroma2.it

The SURFACE (SUrface Residues and Functions Annotated, Compared and Evaluated, URL http://cbm.bio.uniroma2.it/surface/) database is a repository of annotated and compared protein surface regions. SURFACE contains the results of a large-scale protein annotation and local structural comparison project. A non-redundant set of protein chains is used to build a database of protein surface patches, defined as putative surface functional sites. Each patch is annotated with sequence and structure-derived information about function or interaction abilities. A new procedure for structure comparison is used to perform an all-versus-all patches comparison. Selection of the results obtained with stringent parameters offers a similarity score that can be used to associate different patches and allows reliable annotation by similarity. Annotation exerted through the comparison of regions of protein surface allows the highlighting of similarities that cannot be recognized by other methods of sequence or structure comparison. A graphic representation of the surface patches, functional annotations and the structural superpositions is available through the web interface.


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