InterPro, progress and status in 2005

N. J. Mulder; L. Cerutti; R. Copley; E. Courcelle; U. Das; R. Durbin; W. Fleischmann; J. Gough; D. Haft; N. Harte; N. Hulo; R. Apweiler; D. Kahn; A. Kanapin; M. Krestyaninova; D. Lonsdale; R. Lopez; I. Letunic; M. Madera; J. Maslen; J. McDowall; A. Mitchell; T. K. Attwood; A. N. Nikolskaya; S. Orchard; M. Pagni; C. P. Ponting; E. Quevillon; J. Selengut; C. J. Sigrist; V. Silventoinen; D. J. Studholme; R. Vaughan; A. Bairoch; C. H. Wu; A. Bateman; D. Binns; P. Bradley; P. Bork; P. Bucher

InterPro, progress and status in 2005

N. J. Mulder, L. Cerutti, R. Copley, E. Courcelle, U. Das, R. Durbin, W. Fleischmann, J. Gough, D. Haft, N. Harte, N. Hulo, R. Apweiler, D. Kahn, A. Kanapin, M. Krestyaninova, D. Lonsdale, R. Lopez, I. Letunic, M. Madera, J. MaslenJ. McDowall, A. Mitchell, T. K. Attwood, A. N. Nikolskaya, S. Orchard, M. Pagni, C. P. Ponting, E. Quevillon, J. Selengut, C. J. Sigrist, V. Silventoinen, D. J. Studholme, R. Vaughan, A. Bairoch, C. H. Wu, A. Bateman, D. Binns, P. Bradley, P. Bork, P. Bucher

Department of Computer Science

Research output: Contribution to journal › Article (Academic Journal) › peer-review

465 Citations (Scopus)

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).

Translated title of the contribution	InterPro, progress and status in 2005
Original language	English
Article number	-201
Journal	Nucleic Acids Research
Volume	33
Publication status	Published - 2005

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Other identifier: 1040007

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Mulder, N. J., Cerutti, L., Copley, R., Courcelle, E., Das, U., Durbin, R., Fleischmann, W., Gough, J., Haft, D., Harte, N., Hulo, N., Apweiler, R., Kahn, D., Kanapin, A., Krestyaninova, M., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., ... Bucher, P. (2005). InterPro, progress and status in 2005. Nucleic Acids Research, 33, Article -201. http://www.cs.bris.ac.uk/Publications/pub_master.jsp?id=1040007

@article{e0831bc27d954169a221ff72bb881d03,

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).",

author = "Mulder, {N. J.} and L. Cerutti and R. Copley and E. Courcelle and U. Das and R. Durbin and W. Fleischmann and J. Gough and D. Haft and N. Harte and N. Hulo and R. Apweiler and D. Kahn and A. Kanapin and M. Krestyaninova and D. Lonsdale and R. Lopez and I. Letunic and M. Madera and J. Maslen and J. McDowall and A. Mitchell and Attwood, {T. K.} and Nikolskaya, {A. N.} and S. Orchard and M. Pagni and Ponting, {C. P.} and E. Quevillon and J. Selengut and Sigrist, {C. J.} and V. Silventoinen and Studholme, {D. J.} and R. Vaughan and A. Bairoch and Wu, {C. H.} and A. Bateman and D. Binns and P. Bradley and P. Bork and P. Bucher",

note = "Other identifier: 1040007",

year = "2005",

language = "English",

volume = "33",

journal = "Nucleic Acids Research",

issn = "1362-4962",

publisher = "Oxford University Press",

}

Mulder, NJ, Cerutti, L, Copley, R, Courcelle, E, Das, U, Durbin, R, Fleischmann, W, Gough, J, Haft, D, Harte, N, Hulo, N, Apweiler, R, Kahn, D, Kanapin, A, Krestyaninova, M, Lonsdale, D, Lopez, R, Letunic, I, Madera, M, Maslen, J, McDowall, J, Mitchell, A, Attwood, TK, Nikolskaya, AN, Orchard, S, Pagni, M, Ponting, CP, Quevillon, E, Selengut, J, Sigrist, CJ, Silventoinen, V, Studholme, DJ, Vaughan, R, Bairoch, A, Wu, CH, Bateman, A, Binns, D, Bradley, P, Bork, P & Bucher, P 2005, 'InterPro, progress and status in 2005', Nucleic Acids Research, vol. 33, -201. <http://www.cs.bris.ac.uk/Publications/pub_master.jsp?id=1040007>

TY - JOUR

T1 - InterPro, progress and status in 2005

AU - Mulder, N. J.

AU - Cerutti, L.

AU - Copley, R.

AU - Courcelle, E.

AU - Das, U.

AU - Durbin, R.

AU - Fleischmann, W.

AU - Gough, J.

AU - Haft, D.

AU - Harte, N.

AU - Hulo, N.

AU - Apweiler, R.

AU - Kahn, D.

AU - Kanapin, A.

AU - Krestyaninova, M.

AU - Lonsdale, D.

AU - Lopez, R.

AU - Letunic, I.

AU - Madera, M.

AU - Maslen, J.

AU - McDowall, J.

AU - Mitchell, A.

AU - Attwood, T. K.

AU - Nikolskaya, A. N.

AU - Orchard, S.

AU - Pagni, M.

AU - Ponting, C. P.

AU - Quevillon, E.

AU - Selengut, J.

AU - Sigrist, C. J.

AU - Silventoinen, V.

AU - Studholme, D. J.

AU - Vaughan, R.

AU - Bairoch, A.

AU - Wu, C. H.

AU - Bateman, A.

AU - Binns, D.

AU - Bradley, P.

AU - Bork, P.

AU - Bucher, P.

N1 - Other identifier: 1040007

PY - 2005

Y1 - 2005

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).

M3 - Article (Academic Journal)

SN - 1362-4962

VL - 33

JO - Nucleic Acids Research

JF - Nucleic Acids Research

M1 - -201

ER -

InterPro, progress and status in 2005

Abstract

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