InterPro in 2011: new developments in the family and domain prediction database

InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing individual protein sequences. Herein we give an overview of new developments in the database and its associated software since 2009, including updates to database content, curation processes and Web and programmatic interfaces.

[1]  L. Holm,et al.  The Pfam protein families database , 2011, Nucleic Acids Res..

[2]  Suzanne M. Paley,et al.  The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases , 2011, Nucleic Acids Res..

[3]  Anne Morgat,et al.  UniPathway: a resource for the exploration and annotation of metabolic pathways , 2011, Nucleic Acids Res..

[4]  Maria Jesus Martin,et al.  Dasty3, a WEB framework for DAS , 2011, Bioinform..

[5]  Philip Jones,et al.  The InterPro BioMart: federated query and web service access to the InterPro Resource , 2011, Database J. Biol. Databases Curation.

[6]  Cyrus Chothia,et al.  SUPERFAMILY 1.75 including a domain-centric gene ontology method , 2010, Nucleic Acids Res..

[7]  María Martín,et al.  Ongoing and future developments at the Universal Protein Resource , 2010, Nucleic Acids Res..

[8]  C. Mungall,et al.  Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development , 2010, BMC Bioinformatics.

[9]  Rodrigo Lopez,et al.  A new bioinformatics analysis tools framework at EMBL–EBI , 2010, Nucleic Acids Res..

[10]  Anushya Muruganujan,et al.  PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium , 2009, Nucleic Acids Res..

[11]  Christine A. Orengo,et al.  Gene3D: merging structure and function for a Thousand genomes , 2009, Nucleic Acids Res..

[12]  Neil D. Rawlings,et al.  MEROPS: the peptidase database , 2009, Nucleic Acids Res..

[13]  Susumu Goto,et al.  KEGG for representation and analysis of molecular networks involving diseases and drugs , 2009, Nucleic Acids Res..

[14]  Amos Bairoch,et al.  PROSITE, a protein domain database for functional characterization and annotation , 2009, Nucleic Acids Res..

[15]  Irina M. Armean,et al.  The IntAct molecular interaction database in 2010 , 2009, Nucleic Acids Res..

[16]  Lincoln Stein,et al.  Reactome knowledgebase of human biological pathways and processes , 2008, Nucleic Acids Res..

[17]  Peer Bork,et al.  SMART 6: recent updates and new developments , 2008, Nucleic Acids Res..

[18]  Elisabeth Coudert,et al.  HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot , 2008, Nucleic Acids Res..

[19]  Hagen Blankenburg,et al.  Integrating biological data – the Distributed Annotation System , 2008, BMC Bioinformatics.

[20]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[21]  Michelle G. Giglio,et al.  TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes , 2006, Nucleic Acids Res..

[22]  Haruki Nakamura,et al.  The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data , 2006, Nucleic Acids Res..

[23]  Cathy H. Wu,et al.  PIRSF Family Classification System for Protein Functional and Evolutionary Analysis , 2006, Evolutionary bioinformatics online.

[24]  Rolf Apweiler,et al.  InterProScan: protein domains identifier , 2005, Nucleic Acids Res..

[25]  Sébastien Carrère,et al.  The ProDom database of protein domain families: more emphasis on 3D , 2004, Nucleic Acids Res..

[26]  C. Claudel-Renard,et al.  Enzyme-specific profiles for genome annotation: PRIAM. , 2003, Nucleic acids research.

[27]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[28]  Peter D'Eustachio,et al.  Reactome knowledgebase of human biological pathways and processes. , 2011, Methods in molecular biology.

[29]  Terri K. Attwood,et al.  PRINTS and its automatic supplement, prePRINTS , 2003, Nucleic Acids Res..

[30]  Amos Bairoch,et al.  The ENZYME database in 2000 , 2000, Nucleic Acids Res..