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Bioinformatics Advance Access published online on September 7, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti011
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 20, 2004
Revised August 9, 2004
Accepted August 29, 2004

Article

iPfam: visualisation of protein-protein interactions in PDB at domain and amino acid resolutions

Robert D. Finn 1*, Mhairi Marshall 1, and Alex Bateman 1

1 The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK

* To whom correspondence should be addressed. E-mail: rdf{at}sanger.ac.uk.


  Abstract

Summary: There are many resources that contain information about binary interactions between proteins. However, protein interactions are defined by only a subset of residues in any protein. We have implemented a web resource that allows the investigation of protein interactions in PDB structures at the level of Pfam domains and amino acid residues. This detailed knowledge relies on the fact that there are a large number of multidomain proteins and protein complexes being deposited in the structure databases. The resource called iPfam is hosted within the Pfam UK website. Most resources focus on the interactions between proteins; iPfam includes these as well as interactions between domains in a single protein.

Availability: iPfam is available on the web for browsing at http://www.sanger.ac.uk/Software/Pfam/iPfam/; the source-data for iPfam is freely available in relational tables via the ftp site ftp://ftp.sanger.ac.uk/pub/databases/Pfam/database_files/.


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