iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions
- Resource Type
- Authors
- Alex Bateman; Robert D. Finn; Mhairi Marshall
- Source
- Bioinformatics (Oxford, England). 21(3)
- Subject
- Statistics and Probability
Models, Molecular
Computer science
Protein Data Bank (RCSB PDB)
Computational biology
Biochemistry
Protein–protein interaction
Domain (software engineering)
World Wide Web
User-Computer Interface
Protein structure
Protein Interaction Mapping
Computer Simulation
Binding site
Amino acid residue
Amino Acids
Databases, Protein
Molecular Biology
chemistry.chemical_classification
Internet
Binding Sites
Proteins
computer.file_format
Protein Data Bank
Computer Science Applications
Amino acid
Visualization
Protein Structure, Tertiary
Computational Mathematics
Computational Theory and Mathematics
chemistry
Models, Chemical
computer
Software
Protein Binding
- Language
- ISSN
- 1367-4803
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@sanger.ac.uk