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Nucleic Acids Research 2005 33(Web Server Issue):W89-W93; doi:10.1093/nar/gki414
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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}oupjournals.org

Article

ProFunc: a server for predicting protein function from 3D structure

Roman A. Laskowski*, James D. Watson and Janet M. Thornton

European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

*To whom correspondence should be addressed. Tel: +44 1223 492 542; Fax: +44 1223 494 468; Email: roman{at}ebi.ac.uk

Received February 15, 2005. Revised March 21, 2005. Accepted March 21, 2005.

ProFunc (http://www.ebi.ac.uk/thornton-srv/databases/ProFunc) is a web server for predicting the likely function of proteins whose 3D structure is known but whose function is not. Users submit the coordinates of their structure to the server in PDB format. ProFunc makes use of both existing and novel methods to analyse the protein's sequence and structure identifying functional motifs or close relationships to functionally characterized proteins. A summary of the analyses provides an at-a-glance view of what each of the different methods has found. More detailed results are available on separate pages. Often where one method has failed to find anything useful another may be more forthcoming. The server is likely to be of most use in structural genomics where a large proportion of the proteins whose structures are solved are of hypothetical proteins of unknown function. However, it may also find use in a comparative analysis of members of large protein families. It provides a convenient compendium of sequence and structural information that often hold vital functional clues to be followed up experimentally.


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