iPfam


24297255	iPfam: a database of protein family and domain interactions found in the Protein Data Bank. [PMID: 24297255] Finn RD, Miller BL, Clements J, Bateman A. Abstract The database iPfam, available at http://ipfam.org, catalogues Pfam domain interactions based on known 3D structures that are found in the Protein Data Bank, providing interaction data at the molecular level. Previously, the iPfam domain-domain interaction data was integrated within the Pfam database and website, but it has now been migrated to a separate database. This allows for independent development, improving data access and giving clearer separation between the protein family and interactions datasets. In addition to domain-domain interactions, iPfam has been expanded to include interaction data for domain bound small molecule ligands. Functional annotations are provided from source databases, supplemented by the incorporation of Wikipedia articles where available. iPfam (version 1.0) contains >9500 domain-domain and 15 500 domain-ligand interactions. The new website provides access to this data in a variety of ways, including interactive visualizations of the interaction data. Nucleic Acids Res. 2014:42(Database issue) \| 97 Citations (from Europe PMC, 2025-03-29)
15353450	iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. [PMID: 15353450] Finn RD, Marshall M, Bateman A. 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 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/. Bioinformatics. 2005:21(3) \| 197 Citations (from Europe PMC, 2025-03-29)

iPfam: a database of protein family and domain interactions found in the Protein Data Bank. [PMID: 24297255]

Finn RD, Miller BL, Clements J, Bateman A.

The database iPfam, available at http://ipfam.org, catalogues Pfam domain interactions based on known 3D structures that are found in the Protein Data Bank, providing interaction data at the molecular level. Previously, the iPfam domain-domain interaction data was integrated within the Pfam database and website, but it has now been migrated to a separate database. This allows for independent development, improving data access and giving clearer separation between the protein family and interactions datasets. In addition to domain-domain interactions, iPfam has been expanded to include interaction data for domain bound small molecule ligands. Functional annotations are provided from source databases, supplemented by the incorporation of Wikipedia articles where available. iPfam (version 1.0) contains >9500 domain-domain and 15 500 domain-ligand interactions. The new website provides access to this data in a variety of ways, including interactive visualizations of the interaction data.

Nucleic Acids Res. 2014:42(Database issue) | 97 Citations (from Europe PMC, 2025-03-29)

iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. [PMID: 15353450]

Finn RD, Marshall M, Bateman A.

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 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/.

Bioinformatics. 2005:21(3) | 197 Citations (from Europe PMC, 2025-03-29)

URL:	http://www.sanger.ac.uk/Software/Pfam/iPfam
Full name:	Catalog of Protein Family Interactions
Description:	The iPfam database is a catalog of protein family interactions, including domain and ligand interactions, calculated from known structures in PDB (Protein Data Bank).
Year founded:	2005
Last update:	2013-6
Version:	v1.0
Accessibility:	Accessible
Country/Region:	United Kingdom

Data type:	Protein
Data object:	NA
Database category:	Interaction
Major species:	NA
Keywords:	domain ligand protein family

University/Institution:	European Bioinformatics Institute
Address:	HHMI Janelia Farm Research Campus, 19700 Helix Drive, Ashburn VA 20147 USA and European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
City:
Province/State:
Country/Region:	United Kingdom
Contact name (PI/Team):	Robert D. Finn
Contact email (PI/Helpdesk):	finnr@janelia.hhmi.org

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Database Commons a catalog of worldwide biological databases