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Bioinformatics Advance Access originally published online on September 7, 2004
Bioinformatics 2005 21(3):410-412; doi:10.1093/bioinformatics/bti011
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Bioinformatics vol. 21 issue 3 © Oxford University Press 2005; all rights reserved.

iPfam: visualization of protein–protein interactions in PDB at domain and amino acid resolutions

Robert D. Finn *, Mhairi Marshall and Alex Bateman

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

*To whom correspondence should be addressed.

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 the Protein Data Bank 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/

Contact: rdf{at}sanger.ac.uk


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