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iPfam specifications


Unique identifier OMICS_02920
Name iPfam
Restrictions to use None
Maintained Yes

Publication for iPfam

iPfam citations


Cross Species Genome Wide Identification of Evolutionary Conserved MicroProteins

Genome Biol Evol
PMCID: 5381583
PMID: 28338802
DOI: 10.1093/gbe/evx041

[…] ins compared with small proteins not containing such domains. To identify and annotate protein–protein interaction domains within microProteins and ancestral proteins, miPFinder utilizes the Pfam and iPfam databases.MiPFinder assigns Pfam domains to all large proteins (hmmscan, cutoff e-value ≤0.1 and c-Evalue ≤0.05), reports domains that have similarity to microProtein candidates (≥60% length of […]


Algorithmic approaches to protein protein interaction site prediction

PMCID: 4338852
PMID: 25713596
DOI: 10.1186/s13015-015-0033-9

[…] f two amino acid substitution matrices: one describing PPISs or protein binding interfaces (PBIs), and the other describing non-protein binding interfaces (NPBIs) or non-PPISs (NPPISs), via MSAs from iPFAM []. These matrices, MPBI and MNPBI respectively, are computed by counting substitutions with pairwise alignment sets [], followed by construction with the BLOSUM method [].Then, for a given quer […]


Comparing human–Salmonella with plant–Salmonella protein–protein interaction predictions

Front Microbiol
PMCID: 4309195
PMID: 25674082
DOI: 10.3389/fmicb.2015.00045

[…] ned by sequence and/or domain comparison to proteins of known interactions (; ; ). Thus, interolog approaches make use of available information from sequence, domain, and PPI databases. Whereas used iPfam and DIP databases as information input to their approach, used DIMA 3.0 and SIMAP databases and obtained domain information from iPfam and 3DID databases, protein sequence information from uni […]


Toward a systems level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria

Front Genet
PMCID: 4079066
PMID: 25071821
DOI: 10.3389/fgene.2014.00191

[…] ein-protein interactions extracted from the databases STRING (2658 proteins, 26,805 interactions), PSIMAP-based (1028 proteins, 12,748 interactions), InterDom (1760 proteins, 80,319 interactions) and iPfAM (1541 proteins, 13,448 interactions) (Kim et al., ). The SynechoNET visualization interface also permits the exploration of a “high confidence” sub-network composed of 509 proteins, common to al […]


Drug Like Protein–Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology

Mol Inform
PMCID: 4160817
PMID: 25254076
DOI: 10.1002/minf.201400040

[…] uctural information can be found at the Protein Data Bank (PDB) and for instance PISite collects interface data from the PDB.[] Structures of domain-domain interactions are available from 3did,[] and iPfam,[] while a spatial classification of 3D protein domain interaction database, KBDOCK, has recently been reported.[] The database Instruct contains high-quality 3D structurally resolved protein in […]


Improved multi level protein–protein interaction prediction with semantic based regularization

BMC Bioinformatics
PMCID: 4004462
PMID: 24725682
DOI: 10.1186/1471-2105-15-103

[…] extracted from Y2H and TAP-MS data. The gold standard of positive interactions was constructed by aggregating experimentally verified or structurally determined interactions taken from MIPS, DIP, and iPfam.• At the domain level, the dataset includes both features for domain families and for domain instances based on frequencies of domains within one or more species and phylogenetic correlations of […]


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iPfam institution(s)
HHMI Janelia Farm Research Campus, Ashburn VA, USA; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

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