InterPro in 2017—beyond protein family and domain annotations

By Robert D. Finn, T. Attwood, Patricia C. Babbitt, Alex Bateman, Peer Bork, A. Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, M. Fraser and 37 more. 2016

1,390 citations recorded by the source corpus.

InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder. These developments enrich the annotations provided by InterPro, increase the overall number of residues annotated and allow more specific functional inferences.

Subfields: Molecular Biology, Computational Biology & Bioinformatics

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Citations in the corpus

The Pfam protein families database in 2019 (2018, background): “is part of the InterPro consortium, an amalgamation of 14 different expert databases (20), which present a single, unified view of regions of functional importance in protein sequences.”
IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding (2018, background): “However, integration into several resources, such as MobiDBlite (41), MobiDB 3.0 (42) and InterPro (43) made it necessary to implement several minor bug-fixes.”
HMMER web server: 2018 update (2018, methodology): “As well as the HMMER website, this library is also being used in the next revision of the InterPro (8) website.”
The EBI search engine: EBI search as a service—making biological data accessible for all (2017, background): “1101/049205); the EBI Metagenomics portal (7) and annotations from the InterPro protein domain and families consortium (8).”
InterPro in 2019: improving coverage, classification and access to protein sequence annotations (2018, background): “Details of InterPro releases and the member database updates integrated into the resource since our last report (31) are given in Table 1.”
MobiDB 3.0: more annotations for intrinsic disorder, conformational diversity and interactions in proteins (2017, methodology): “It has recently joined the InterPro consortium to provide disorder annotation alongside protein domains and families (62).”
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures (2016, background): “The CDD group has started a collaboration with the InterPro group at the European Bioinformatics Institute to supplement sequence annotation provided by InterPro with data that are uniquely provided by NCBI’s CDD curation effort, including protein domain models for very specific subfamilies and the ”
20 years of the SMART protein domain annotation resource (2017, background): “Many of these, including SMART, are integrated into InterPro (16).”
The InterPro protein families and domains database: 20 years on (2020, background): “We previously reported that 78.4% of sequences in the UniProt Archive (UniParc) were annotated by InterPro (23).”
The Human Transcription Factors. (2018, positive): “We manually examined 2,765 proteins compiled by combining putative TF lists from several sources: the aforementioned papers (Fulton et al., 2009; Vaquerizas et al., 2009), domain searches (using HMMs and parameters from CisBP [Weirauch et al., 2014] and Interpro, as well as the TRANSFAC-related data”
agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update (2017, background): “The InterPro (37) ID and Pfam (38) accessions have internal connections with the GO.”
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools (2018, methodology): “To address this problem, in collaboration with InterPro (20) and UniProt Reference Proteomes (21), we have implemented a solution to support over 800 additional genomes on the PANTHER website.”