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InterPro: An integrated documentation resource for protein families, domains and functional sites

2002 Briefings in Bioinformatics  
In recognition of this, InterPro was developed as an integrated documentation resource for protein families, domains and functional sites, to rationalise the complementary efforts of the individual protein  ...  Release 4.0 of InterPro (November 2001) contains 4,691 entries, representing 3,532 families, 1,068 domains, 74 repeats and 15 sites of posttranslational modification (PTMs) encoded by different regular  ...  Acknowledgements The InterPro project is supported by the ProFuSe grant (number QLG2-CT-2000-00517) of the European Commission.  ... 
doi:10.1093/bib/3.3.225 pmid:12230031 fatcat:2igbmarmcjbpfphuwf6l7ny4cy

The InterPro database, an integrated documentation resource for protein families, domains and functional sites

R. Apweiler
2001 Nucleic Acids Research  
InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects.  ...  Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function.  ...  ACKNOWLEDGEMENTS The InterPro project is supported by grant number BIO4-CT98-0052 of the European Commission. T.K.A. is a Royal Society University Research Fellow.  ... 
doi:10.1093/nar/29.1.37 pmid:11125043 pmcid:PMC29841 fatcat:ft4lb3l2zjhnph2ll42i3jnz3e

InterPro--an integrated documentation resource for protein families, domains and functional sites

R. Apweiler, T. K. Attwood, A. Bairoch, A. Bateman, E. Birney, M. Biswas, P. Bucher, L. Cerutti, F. Corpet, M. D. R. Croning, R. Durbin, L. Falquet (+16 others)
2000 Bioinformatics  
Motivation: InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed initially as a means of rationalising the complementary efforts of the PROSITE  ...  Release 1.2 of InterPro (June 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification (PTMs) encoded by 6581 different regular expressions  ...  Acknowledgements The InterPro project is supported by grant number BIO4-CT98-0052 of the European Commission. TKA is a Royal Society University Research Fellow.  ... 
doi:10.1093/bioinformatics/16.12.1145 pmid:11159333 fatcat:zz6c5bhuwbhlfofasde65zj7ku

Website Review: InterPro (The Integrated Resource of Protein Domains and Functional Sites). http://www.ebi.ac.uk/interpro/

Christopher Southan
2000 Yeast  
The family and motif databases, PROSITE, PRINTS, Pfam and ProDom, have been integrated into a powerful resource for protein secondary annotation.  ...  The website links can be used to analyse novel sequences and for queries across the proteomes of 32 organisms, including the partial human set, by domain and/or protein family.  ...  Other members of the project team are listed on the website at http://www.ebi.ac.uk/interpro/release_notes.html. Source databases  ... 
doi:10.1002/1097-0061(200012)17:4<327::aid-yea45>3.3.co;2-b pmid:11119311 pmcid:PMC2448387 fatcat:37anj5oo5ra65lnckr6vvsmvye

InterPro, progress and status in 2005

N. J. Mulder
2004 Nucleic Acids Research  
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created to integrate the major protein signature databases.  ...  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.  ...  ACKNOWLEDGEMENTS The InterPro project is supported by the ProFuSe grant (number QLG2-CT-2000-00517) and the Integr8 grant (number QLRI-CT-2001000015) of the European Commission.  ... 
doi:10.1093/nar/gki106 pmid:15608177 pmcid:PMC540060 fatcat:ykhpocbakfck3elxzhjb7z34rm

HMM-based databases in InterPro

A. Bateman
2002 Briefings in Bioinformatics  
Protein family databases are an important resource for protein annotation and understanding protein evolution and function.  ...  In recent years hidden Markov models (HMMs) have become one of the key technologies used for detection of members of these families.  ...  Through the mechanism of InterPro 22 the results from searches of these different resources can be easily integrated allowing a comprehensive view of protein architecture and function.  ... 
doi:10.1093/bib/3.3.236 pmid:12230032 fatcat:ykxhgzgngrbblmc3zbwdrpsf7q

InterPro (The Integrated Resource of Protein Domains and Functional Sites)

Christopher Southan
2000 Yeast  
The family and motif databases, PROSITE, PRINTS, Pfam and ProDom, have been integrated into a powerful resource for protein secondary annotation.  ...  The website links can be used to analyse novel sequences and for queries across the proteomes of 32 organisms, including the partial human set, by domain and/or protein family.  ...  Other members of the project team are listed on the website at http://www.ebi.ac.uk/interpro/release_notes.html. Source databases  ... 
doi:10.1002/1097-0061(200012)17:4<327::aid-yea45>3.0.co;2-k fatcat:y52i3tf7fjavbfcvgvaefvudsq

The InterPro Database, 2003 brings increased coverage and new features

N. J. Mulder
2003 Nucleic Acids Research  
InterPro, an integrated documentation resource of protein families, domains and functional sites, was created in 1999 as a means of amalgamating the major protein signature databases into one comprehensive  ...  resource.  ...  This integration will enhance the capability of the database in the field of protein classification and characterisation and make the database, a true integrated resource for complete protein sequence  ... 
doi:10.1093/nar/gkg046 pmid:12520011 pmcid:PMC165493 fatcat:fy5hcc4yxvgtpgniyqtsnwmqvm

Interactive InterPro-based comparisons of proteins in whole genomes

A. Kanapin, R. Apweiler, M. Biswas, W. Fleischmann, Y. Karavidopoulou, P. Kersey, E. V. Kriventseva, V. Mittard, N. Mulder, T. Oinn, I. Phan, F. Servant (+1 others)
2002 Bioinformatics  
Motivation: The SWISS-PROT group at the EBI has developed the Proteome Analysis Database utilizing existing resources and providing comprehensive and integrated comparative analysis of the predicted protein  ...  The Proteome Analysis Database is accompanied by a program that has been designed to carry out interactive InterPro proteome comparisons for any one proteome against any other one or more of the proteomes  ...  COGs group together related proteins with similar but sometimes non-identical functions InterPro (http://www.ebi.ac.uk/interpro/) is an integrated documentation resource of protein families, domains and  ... 
doi:10.1093/bioinformatics/18.2.374 pmid:11847096 fatcat:zyagz24525eo3nyjimdhw27xw4

The InterPro protein families and domains database: 20 years on

Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasaamy, Alex Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj, Lorna Richardson, Gustavo A Salazar (+21 others)
2020 Nucleic Acids Research  
The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites.  ...  Founded in 1999, InterPro has become one of the most widely used resources for protein family annotation.  ...  and Siew-Yit Yong.  ... 
doi:10.1093/nar/gkaa977 pmid:33156333 pmcid:PMC7778928 fatcat:vfs7k3dxr5bcpbpvxbptj6r46m

The InterPro protein families database: the classification resource after 15 years

Alex Mitchell, Hsin-Yu Chang, Louise Daugherty, Matthew Fraser, Sarah Hunter, Rodrigo Lopez, Craig McAnulla, Conor McMenamin, Gift Nuka, Sebastien Pesseat, Amaia Sangrador-Vegas, Maxim Scheremetjew (+24 others)
2014 Nucleic Acids Research  
Here, we report on the status of InterPro Figure 1. InterPro matches for UniProtKB entry Q3JCG5 showing predicted protein family membership, domains and sites.  ...  to classify protein families and domains.  ...  The aim of InterPro is to combine their individual strengths to provide a single resource, through which scientists can access comprehensive information about protein families, domains and functional sites  ... 
doi:10.1093/nar/gku1243 pmid:25428371 pmcid:PMC4383996 fatcat:4asvzb32obgwhlvdkrfhiokvme

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

S. Hunter, P. Jones, A. Mitchell, R. Apweiler, T. K. Attwood, A. Bateman, T. Bernard, D. Binns, P. Bork, S. Burge, E. de Castro, P. Coggill (+45 others)
2012 Nucleic Acids Research  
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  ...  InterPro has utility in the large-scale analysis of whole genomes and metagenomes, as well as in characterizing individual protein sequences.  ...  protein families, domains, sites and repeats.  ... 
doi:10.1093/nar/gks456 pmcid:PMC3378909 fatcat:oqmafftblfcmdgh4a3i4nzqpzu

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

S. Hunter, P. Jones, A. Mitchell, R. Apweiler, T. K. Attwood, A. Bateman, T. Bernard, D. Binns, P. Bork, S. Burge, E. de Castro, P. Coggill (+38 others)
2011 Nucleic Acids Research  
protein families, domains, sites and repeats.  ...  The aim of InterPro is to combine their individual strengths to provide a single resource through which scientists can access comprehensive information about protein families, domains and functional sites  ... 
doi:10.1093/nar/gkr948 pmid:22096229 pmcid:PMC3245097 fatcat:awtdl7qobjhnveofe7jxno6ju4

Proteome Analysis Database: online application of InterPro and CluSTr for the functional classification of proteins in whole genomes

R. Apweiler
2001 Nucleic Acids Research  
The two main projects used, InterPro and CluSTr, give a new perspective on families, domains and sites and cover 31-67% (InterPro statistics) of the proteins from each of the complete genomes.  ...  The SWISS-PROT group at EBI has developed the Proteome Analysis Database utilising existing resources and providing comparative analysis of the predicted protein coding sequences of the complete genomes  ...  InterPro InterPro (http://www.ebi.ac.uk/interpro/) (9) is an integrated documentation resource of protein families, domains and functional sites that has been developed initially as a means of rationalising  ... 
doi:10.1093/nar/29.1.44 pmid:11125045 pmcid:PMC29822 fatcat:ug42g6zpf5bsfoam7zavbsvlki

Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation

S. Burge, E. Kelly, D. Lonsdale, P. Mutowo-Muellenet, C. McAnulla, A. Mitchell, A. Sangrador-Vegas, S.-Y. Yong, N. Mulder, S. Hunter
2012 Database: The Journal of Biological Databases and Curation  
We describe a revised protocol for GO mapping that enables us to assign GO terms to domains based on the function of the individual domain, rather than the function of the families in which the domain  ...  The InterPro2GO mappings are comprised of the cross-references between these two resources and are the largest source of GO annotation predictions for proteins.  ...  Acknowledgements We thank Emily Dimmer and Claire O'Donovan for their critical reading of this manuscript and Tony Sawford for assistance with protein match counts. Conflict of interest.  ... 
doi:10.1093/database/bar068 pmid:22301074 pmcid:PMC3270475 fatcat:mczeyk6qqrhxpn2aysoyqgocde
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