InterPro, progress and status in 2005

Nicola J Mulder; Rolf Apweiler; Teresa K Attwood; Amos Bairoch; Alex Bateman; David Binns; Paul Bradley; Peer Bork; Phillip Bucher; Lorenzo Cerutti; Richard Copley; Emmanuel Courcelle; Ujjwal Das; Richard Durbin; Wolfgang Fleischmann; Julian Gough; Daniel Haft; Nicola Harte; Nicolas Hulo; Daniel Kahn; Alexander Kanapin; Maria Krestyaninova; David Lonsdale; Rodrigo Lopez; Ivica Letunic; Martin Madera; John Maslen; Jennifer McDowall; Alex Mitchell; Anastasia N Nikolskaya; Sandra Orchard; Marco Pagni; Chris P Ponting; Emmanuel Quevillon; Jeremy Selengut; Christian J A Sigrist; Ville Silventoinen; David J Studholme; Robert Vaughan; Cathy H Wu

doi:10.1093/nar/gki106

InterPro, progress and status in 2005

Nicola J Mulder, Rolf Apweiler, Teresa K Attwood, Amos Bairoch, Alex Bateman, David Binns, Paul Bradley, Peer Bork, Phillip Bucher, Lorenzo Cerutti, Richard Copley, Emmanuel Courcelle, Ujjwal Das, Richard Durbin, Wolfgang Fleischmann, Julian Gough, Daniel Haft, Nicola Harte, Nicolas Hulo, Daniel KahnAlexander Kanapin, Maria Krestyaninova, David Lonsdale, Rodrigo Lopez, Ivica Letunic, Martin Madera, John Maslen, Jennifer McDowall, Alex Mitchell, Anastasia N Nikolskaya, Sandra Orchard, Marco Pagni, Chris P Ponting, Emmanuel Quevillon, Jeremy Selengut, Christian J A Sigrist, Ville Silventoinen, David J Studholme, Robert Vaughan, Cathy H Wu

Deanery of Molecular, Genetic and Population Health Sciences

Research output: Contribution to journal › Article › peer-review

Abstract

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).

Original language	English
Pages (from-to)	D201-5
Journal	Nucleic Acids Research
Volume	33
Issue number	Database issue
DOIs	https://doi.org/10.1093/nar/gki106
Publication status	Published - 1 Jan 2005

Keywords

Databases, Protein
Humans
Protein Structure, Tertiary
Proteins
Sequence Alignment
Sequence Analysis, Protein
Systems Integration

Access to Document

10.1093/nar/gki106

Cite this

Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P., Cerutti, L., Copley, R., Courcelle, E., Das, U., Durbin, R., Fleischmann, W., Gough, J., Haft, D., Harte, N., Hulo, N., ... Wu, C. H. (2005). InterPro, progress and status in 2005. Nucleic Acids Research, 33(Database issue), D201-5. https://doi.org/10.1093/nar/gki106

@article{389c9b4baa6047459a7b0b4c0227abcd,

title = "InterPro, progress and status in 2005",

abstract = "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).",

keywords = "Databases, Protein, Humans, Protein Structure, Tertiary, Proteins, Sequence Alignment, Sequence Analysis, Protein, Systems Integration",

author = "Mulder, {Nicola J} and Rolf Apweiler and Attwood, {Teresa K} and Amos Bairoch and Alex Bateman and David Binns and Paul Bradley and Peer Bork and Phillip Bucher and Lorenzo Cerutti and Richard Copley and Emmanuel Courcelle and Ujjwal Das and Richard Durbin and Wolfgang Fleischmann and Julian Gough and Daniel Haft and Nicola Harte and Nicolas Hulo and Daniel Kahn and Alexander Kanapin and Maria Krestyaninova and David Lonsdale and Rodrigo Lopez and Ivica Letunic and Martin Madera and John Maslen and Jennifer McDowall and Alex Mitchell and Nikolskaya, {Anastasia N} and Sandra Orchard and Marco Pagni and Ponting, {Chris P} and Emmanuel Quevillon and Jeremy Selengut and Sigrist, {Christian J A} and Ville Silventoinen and Studholme, {David J} and Robert Vaughan and Wu, {Cathy H}",

year = "2005",

month = jan,

day = "1",

doi = "10.1093/nar/gki106",

language = "English",

volume = "33",

pages = "D201--5",

journal = "Nucleic Acids Research",

issn = "0305-1048",

publisher = "Oxford University Press",

number = "Database issue",

}

Mulder, NJ, Apweiler, R, Attwood, TK, Bairoch, A, Bateman, A, Binns, D, Bradley, P, Bork, P, Bucher, P, Cerutti, L, Copley, R, Courcelle, E, Das, U, Durbin, R, Fleischmann, W, Gough, J, Haft, D, Harte, N, Hulo, N, Kahn, D, Kanapin, A, Krestyaninova, M, Lonsdale, D, Lopez, R, Letunic, I, Madera, M, Maslen, J, McDowall, J, Mitchell, A, Nikolskaya, AN, Orchard, S, Pagni, M, Ponting, CP, Quevillon, E, Selengut, J, Sigrist, CJA, Silventoinen, V, Studholme, DJ, Vaughan, R & Wu, CH 2005, 'InterPro, progress and status in 2005', Nucleic Acids Research, vol. 33, no. Database issue, pp. D201-5. https://doi.org/10.1093/nar/gki106

TY - JOUR

T1 - InterPro, progress and status in 2005

AU - Mulder, Nicola J

AU - Apweiler, Rolf

AU - Attwood, Teresa K

AU - Bairoch, Amos

AU - Bateman, Alex

AU - Binns, David

AU - Bradley, Paul

AU - Bork, Peer

AU - Bucher, Phillip

AU - Cerutti, Lorenzo

AU - Copley, Richard

AU - Courcelle, Emmanuel

AU - Das, Ujjwal

AU - Durbin, Richard

AU - Fleischmann, Wolfgang

AU - Gough, Julian

AU - Haft, Daniel

AU - Harte, Nicola

AU - Hulo, Nicolas

AU - Kahn, Daniel

AU - Kanapin, Alexander

AU - Krestyaninova, Maria

AU - Lonsdale, David

AU - Lopez, Rodrigo

AU - Letunic, Ivica

AU - Madera, Martin

AU - Maslen, John

AU - McDowall, Jennifer

AU - Mitchell, Alex

AU - Nikolskaya, Anastasia N

AU - Orchard, Sandra

AU - Pagni, Marco

AU - Ponting, Chris P

AU - Quevillon, Emmanuel

AU - Selengut, Jeremy

AU - Sigrist, Christian J A

AU - Silventoinen, Ville

AU - Studholme, David J

AU - Vaughan, Robert

AU - Wu, Cathy H

PY - 2005/1/1

Y1 - 2005/1/1

N2 - 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).

AB - 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).

KW - Databases, Protein

KW - Humans

KW - Protein Structure, Tertiary

KW - Proteins

KW - Sequence Alignment

KW - Sequence Analysis, Protein

KW - Systems Integration

U2 - 10.1093/nar/gki106

DO - 10.1093/nar/gki106

M3 - Article

C2 - 15608177

VL - 33

SP - D201-5

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - Database issue

ER -

InterPro, progress and status in 2005

Abstract

Keywords

Access to Document

Fingerprint

Cite this