InterPro, progress and status in 2005

By Nicola J. Mulder, Rolf Apweiler, T. Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, L. Cerutti and 30 more. Nucleic Acids Res., 2004

559 citations recorded by the source corpus.

InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases. Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFAMILY. Signatures are manually integrated into InterPro entries that are curated to provide biological and functional information. Annotation is provided in an abstract, Gene Ontology mapping and links to specialized databases. New features of InterPro include extended protein match views, taxonomic range information and protein 3D structure data. One of the new match views is the InterPro Domain Architecture view, which shows the domain composition of protein matches. Two new entry types were introduced to better describe InterPro entries: these are active site and binding site. PIRSF and the structure-based SUPERFAMILY are the latest member databases to join InterPro, and CATH and PANTHER are soon to be integrated. InterPro release 8.0 contains 11 007 entries, representing 2573 domains, 8166 families, 201 repeats, 26 active sites, 21 binding sites and 20 post-translational modification sites. InterPro covers over 78% of all proteins in the Swiss-Prot and TrEMBL components of UniProt. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro).

Subfields: Materials Chemistry, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/464f28abb94bdaf301b92493206b2bb5b4cd5e8d

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Citations in the corpus

The UCSC Genome Browser Database: update 2006 (2005, background): “Links to Interpro (15) and Pfam (16) provide protein domain and structure information.”
Sequence and structural analysis of BTB domain proteins (2005, methodology): “Arabidsopsis thaliana, Saccharomyces cerevisiae and Schizosaccharomyces pombe protein sequences were retrieved from Uniprot [ 46 ].”
Diet and dioxins: the need to cut back. (2004, background): “Although there are many databases of sequence motifs available [ 20-23 ], these databases were created in a supervised way to have motifs that characterize different known protein families, domains, or functional sites.”
TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes (2005, methodology): “For each release protein sequences are analyzed with Inter-ProScan (18).”
Evolution of Symbiotic Bacteria in the Distal Human Intestine (2007, methodology): “These domains were used to assign a functional identiﬁer (InterPro ID) that was then mapped onto Gene Ontology (GO) terms [12] using InterProScan [13].”
The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families (2007, background): “Many of these classifications, together with various expert-curated databases [19] such as Swiss-Prot [20], Pfam [15,21], and TIGRFAM [22,23], or integrated efforts such as Uniprot [24] and InterPro [ 25 ], provide rich resources for protein annotation.”
MaGe: a microbial genome annotation system supported by synteny results (2006, methodology): “The main purpose of this step is to infer, as precisely as possible, specific function(s) for each individual gene by the completeness of gene products, gene names, Enzyme Commission (EC) numbers and functional classes when possible (Supplementary Figure 1). Assignation of Gene Ontology terms (44) i”
PlasmoDB: a functional genomic database for malaria parasites (2008, background): “evidence of protein–protein interaction (yeast two hybrid and predicted interactome) (27,28), Genome Ontology (GO) (29) and InterPro domain ( 30 ) annotations for P. falciparum, P. vivax, P. berghei, P. yoelii, P. knowlesi and P. chabaudi, Enzyme Commission (EC) number (29) annotation for P. falcipa”
New developments in the InterPro database (2007, background): “InterPro ( 1 ) incorporates the major protein signature databases into a single resource.”
IntAct—open source resource for molecular interaction data (2006, unknown): “We now allow users to highlight interactor sharing the same InterPro ( 9 ) annotation.”
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis (2007, methodology): “…types of gene/protein IDs between NCBI and UniProt systems since different annotation databases use one or another system as their major gene identifier systems, e.g. GeneRif [20] adopts NCBI IDs as major associated identifiers; InterPro [21] uses UniProt/SwissProt as major associated identifiers.”
MODOMICS: a database of RNA modification pathways. 2008 update (2008, background): “If sequences are available, the name of the corresponding ORF and accession numbers for the Swiss-Prot (8) and NCBI (9) databases are provided.”