InterPro: the integrative protein signature database

By S. Hunter, Rolf Apweiler, T. Attwood, Amos Bairoch, Alex Bateman, David Binns, Peer Bork, Ujjwal Das, L. Daugherty, Lauranne Duquenne and 28 more. 2008

2,089 citations recorded by the source corpus.

The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or ‘signatures’ representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total ∼58 000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein–protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/).

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Generating functional protein variants with variational autoencoders (2020, methodology): “As a practical testbed for deep generative protein design, we chose to work with a dataset of 69,130 homologues of bacterial luciferase obtained from InterPro [34] (IPR011251).”
Accelerated Profile HMM Searches (2011, methodology): “Profile HMM methods have become important only in the niche of protein domain family analysis, where the speed differential is compensated by being able to use a single profile HMM to represent a family of hundreds of homologous individual sequences [10,11].”
The Pfam protein families database (2011, methodology): “We have therefore developed a pipeline to generate stub articles automatically in a Wikipedia ‘sandbox’, often taking existing family annotations from the InterPro database (9) as the basis for the article.”
The Protein Model Portal—a comprehensive resource for protein structure and model information (2013, background): “Information about available experimental structures of the query protein are also provided as well as biological (38) and domain architecture annotations (39) (Figure 2).”
How Common Is Disorder? Occurrence of Disordered Residues in Four Domains of Life (2015, methodology): “To this end, several databases are currently available: PROSITE, InterPro, Pfam, and ModiDP [1–4].”
The UniProt-GO Annotation database in 2011 (2011, methodology): “UniProt is the main supplier of electronic GO annotation predictions to the GO Consortium via close collaboration with independent annotation efforts in the InterPro (15), Ensembl Genomes (16) and Ensembl (17) projects.”
The IntAct molecular interaction database in 2010 (2009, background): “Binding sites are also crossreferenced to the InterPro database (13), whenever possible.”
Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal (2012, methodology): “Protein sequence structure and function annotation programs: InterProScan (60) for protein domain motifs and families recognition, PsiPred (61) for secondary structure prediction, DisoPred (62) for disorder prediction and MEMSAT (63) to predict transmembrane segments.”
Ensembl 2012 (2011, methodology): “We integrate these annotations with a large number of external data sources including InterPro (2), UniProt (3) and Pfam (4).”
Data Mining Techniques for the Life Sciences (2010, background): “Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., Lopez, R. (2005) InterProScan: protein domains identifier.”
The genome of Eucalyptus grandis (2014, background): “A total of 133 amino acid sequences from Eucalyptus grandis (50), Vitis vinifera (34), Populus trichocarpa (40), Arabidopsis thaliana (6) and Oryza sativa (3) corresponding to three woody-expanded (subgroups 5, 6 and AtMYB5 based on Arabidopsis classification) and five woody-preferential subgroups (”
HMMER web server: interactive sequence similarity searching (2011, methodology): “The HMMER software suite has been widely used, particularly by protein family databases such as Pfam (1) and InterPro (2) and their associated search tools.”
Producing more with less: Strategies and novel technologies for plant-based food biofortification (2013, methodology): “…rely on tools such as MIRA (Chevreux et al., 2004), Myrna (Langmead, Hansen, & Leek, 2010), MG-RAST (Meyer et al., 2008) or Blast2Go (B2G) (Conesa et al., 2005), whereas proteomic studies frequently utilize InterPro (Hunter et al., 2008) and Mascot (Perkins, Pappin, Creasy, & Cottrell, 1999).”
Reorganizing the protein space at the Universal Protein Resource (UniProt) (2011, background): “uk/ uniprot/biomart/martview) is available which allows complex queries between UniProt and other data resources such as PRIDE (11), Ensembl and InterPro (12).”