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Database Commons - PROSITE

PROSITE

Citations: 8754

z-index 246.41

Short name PROSITE
Full name Database of protein domains, families and functional sites
Description PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them
URL http://prosite.expasy.org/
Year founded 1988
Last update & version 2016-03-09    v20.124
Availability Free to all users
University/Institution hosted Swiss Institute of Bioinformatics
Address 1 rue Michel Servet, 1211 Geneva 4, Switzerland
City Geneva
Province/State
Country/Region Switzerland
Contact name Christian J. A. Sigrist
Contact email prosite-group@isb-sib.ch
Data type(s)
Major organism(s)
Keyword(s)
  • protein domain
  • protein family
Publication(s)
  • New and continuing developments at PROSITE. [PMID: 23161676]

    Christian J A Sigrist, Edouard de Castro, Lorenzo Cerutti, Béatrice A Cuche, Nicolas Hulo, Alan Bridge, Lydie Bougueleret, Ioannis Xenarios
    Nucleic acids research 2013:41(Database issue)
    222 Citations (Google Scholar as of 2016-01-14)

    Abstract: PROSITE (http://prosite.expasy.org/) consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule a collection of rules, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE signatures, together with ProRule, are used for the annotation of domains and features of UniProtKB/Swiss-Prot entries. Here, we describe recent developments that allow users to perform whole-proteome annotation as well as a number of filtering options that can be combined to perform powerful targeted searches for biological discovery. The latest version of PROSITE (release 20.85, of 30 August 2012) contains 1308 patterns, 1039 profiles and 1041 ProRules.

  • PROSITE, a protein domain database for functional characterization and annotation. [PMID: 19858104]

    Christian J A Sigrist, Lorenzo Cerutti, Edouard de Castro, Petra S Langendijk-Genevaux, Virginie Bulliard, Amos Bairoch, Nicolas Hulo
    Nucleic acids research 2010:38(Database issue)
    582 Citations (Google Scholar as of 2016-03-28)

    Abstract: PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE is largely used for the annotation of domain features of UniProtKB/Swiss-Prot entries. Among the 983 (DNA-binding) domains, repeats and zinc fingers present in Swiss-Prot (release 57.8 of 22 September 2009), 696 ( approximately 70%) are annotated with PROSITE descriptors using information from ProRule. In order to allow better functional characterization of domains, PROSITE developments focus on subfamily specific profiles and a new profile building method giving more weight to functionally important residues. Here, we describe AMSA, an annotated multiple sequence alignment format used to build a new generation of generalized profiles, the migration of ScanProsite to Vital-IT, a cluster of 633 CPUs, and the adoption of the Distributed Annotation System (DAS) to facilitate PROSITE data integration and interchange with other sources. The latest version of PROSITE (release 20.54, of 22 September 2009) contains 1308 patterns, 863 profiles and 869 ProRules. PROSITE is accessible at: http://www.expasy.org/prosite/.

  • The 20 years of PROSITE. [PMID: 18003654]

    Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Béatrice A Cuche, Edouard de Castro, Corinne Lachaize, Petra S Langendijk-Genevaux, Christian J A Sigrist
    Nucleic acids research 2008:36(Database issue)
    428 Citations (Google Scholar as of 2016-03-28)

    Abstract: PROSITE consists of documentation entries describing protein domains, families and functional sites, as well as associated patterns and profiles to identify them. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. In this article, we describe the implementation of a new method to assign a status to pattern matches, the new PROSITE web page and a new approach to improve the specificity and sensitivity of PROSITE methods. The latest version of PROSITE (release 20.19 of 11 September 2007) contains 1319 patterns, 745 profiles and 764 ProRules. Over the past 2 years, about 200 domains have been added, and now 53% of UniProtKB/Swiss-Prot entries (release 54.2 of 11 September 2007) have a PROSITE match. PROSITE is available on the web at: http://www.expasy.org/prosite/.

  • The PROSITE database. [PMID: 16381852]

    Nicolas Hulo, Amos Bairoch, Virginie Bulliard, Lorenzo Cerutti, Edouard De Castro, Petra S Langendijk-Genevaux, Marco Pagni, Christian J A Sigrist
    Nucleic acids research 2006:34(Database issue)
    743 Citations (Google Scholar as of 2016-03-28)

    Abstract: The PROSITE database consists of a large collection of biologically meaningful signatures that are described as patterns or profiles. Each signature is linked to a documentation that provides useful biological information on the protein family, domain or functional site identified by the signature. The PROSITE database is now complemented by a series of rules that can give more precise information about specific residues. During the last 2 years, the documentation and the ScanProsite web pages were redesigned to add more functionalities. The latest version of PROSITE (release 19.11 of September 27, 2005) contains 1329 patterns and 552 profile entries. Over the past 2 years more than 200 domains have been added, and now 52% of UniProtKB/Swiss-Prot entries (release 48.1 of September 27, 2005) have a cross-reference to a PROSITE entry. The database is accessible at http://www.expasy.org/prosite/.

  • Recent improvements to the PROSITE database. [PMID: 14681377]

    Nicolas Hulo, Christian J A Sigrist, Virginie Le Saux, Petra S Langendijk-Genevaux, Lorenza Bordoli, Alexandre Gattiker, Edouard De Castro, Philipp Bucher, Amos Bairoch
    Nucleic acids research 2004:32(Database issue)
    491 Citations (Google Scholar as of 2016-03-28)

    Abstract: The PROSITE database consists of a large collection of biologically meaningful signatures that are described as patterns or profiles. Each signature is linked to documentation that provides useful biological information on the protein family, domain or functional site identified by the signature. The PROSITE web page has been redesigned and several tools have been implemented to help the user discover new conserved regions in their own proteins and to visualize domain arrangements. We also introduced the facility to search PDB with a PROSITE entry or a user's pattern and visualize matched positions on 3D structures. The latest version of PROSITE (release 18.17 of November 30, 2003) contains 1676 entries. The database is accessible at http://www.expasy.org/prosite/.

  • PROSITE: a documented database using patterns and profiles as motif descriptors. [PMID: 12230035]

    Christian J A Sigrist, Lorenzo Cerutti, Nicolas Hulo, Alexandre Gattiker, Laurent Falquet, Marco Pagni, Amos Bairoch, Philipp Bucher
    Briefings in bioinformatics 2002:3(3)
    741 Citations (Google Scholar as of 2016-03-28)

    Abstract: Among the various databases dedicated to the identification of protein families and domains, PROSITE is the first one created and has continuously evolved since. PROSITE currently consists of a large collection of biologically meaningful motifs that are described as patterns or profiles, and linked to documentation briefly describing the protein family or domain they are designed to detect. The close relationship of PROSITE with the SWISS-PROT protein database allows the evaluation of the sensitivity and specificity of the PROSITE motifs and their periodic reviewing. In return, PROSITE is used to help annotate SWISS-PROT entries. The main characteristics and the techniques of family and domain identification used by PROSITE are reviewed in this paper.

  • The PROSITE database, its status in 2002. [PMID: 11752303]

    Laurent Falquet, Marco Pagni, Philipp Bucher, Nicolas Hulo, Christian J A Sigrist, Kay Hofmann, Amos Bairoch
    Nucleic acids research 2002:30(1)
    1141 Citations (Google Scholar as of 2016-03-28)

    Abstract: PROSITE [Bairoch and Bucher (1994) Nucleic Acids Res., 22, 3583-3589; Hofmann et al. (1999) Nucleic Acids Res., 27, 215-219] is a method of identifying the functions of uncharacterized proteins translated from genomic or cDNA sequences. The PROSITE database (http://www.expasy.org/prosite/) consists of biologically significant patterns and profiles designed in such a way that with appropriate computational tools it can rapidly and reliably help to determine to which known family of proteins (if any) a new sequence belongs, or which known domain(s) it contains.

  • The PROSITE database, its status in 1999. [PMID: 9847184]

    K Hofmann, P Bucher, L Falquet, A Bairoch
    Nucleic acids research 1999:27(1)
    1241 Citations (Google Scholar as of 2016-03-28)

    Abstract: The PROSITE database (http://www.expasy.ch/sprot/prosite.htm l) consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of protein (if any) a new sequence belongs, or which known domain(s) it contains.

  • The PROSITE database, its status in 1997. [PMID: 9016539]

    A Bairoch, P Bucher, K Hofmann
    Nucleic acids research 1997:25(1)
    969 Citations (Google Scholar as of 2016-03-28)

    Abstract: The PROSITE database consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of protein (if any) a new sequence belongs, or which known domain(s) it contains.

  • The PROSITE database, its status in 1995. [PMID: 8594577]

    A Bairoch, P Bucher, K Hofmann
    Nucleic acids research 1996:24(1)
    360 Citations (Google Scholar as of 2016-03-28)

    Abstract: The PROSITE database consists of biologically significant patterns and profiles formulated in such a way that with appropriate computational tools it can help to determine to which known family of proteins (if any) a new sequence belongs or which known domain(s) it contains.

  • PROSITE: recent developments. [PMID: 7937064]

    A Bairoch, P Bucher
    Nucleic acids research 1994:22(17)
    234 Citations (Google Scholar as of 2016-03-28)

    Abstract: PROSITE is a compilation of sites and patterns found in protein sequences; it can be used as a method of determining the function of uncharacterized proteins translated from genomic or cDNA sequences.

  • The PROSITE dictionary of sites and patterns in proteins, its current status. [PMID: 8332530]

    A Bairoch
    Nucleic acids research 1993:21(13)
    365 Citations (Google Scholar as of 2016-03-28)

    Abstract:

  • PROSITE: a dictionary of sites and patterns in proteins. [PMID: 1598232]

    A Bairoch
    Nucleic acids research 1992:20 Suppl
    573 Citations (Google Scholar as of 2016-03-28)

    Abstract:

  • PROSITE: a dictionary of sites and patterns in proteins. [PMID: 2041810]

    A Bairoch
    Nucleic acids research 1991:19 Suppl
    664 Citations (Google Scholar as of 2016-03-28)

    Abstract:

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Rate of accessibility:
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200 OK2018-01-30
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200 OK2018-01-19
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200 OK2018-01-02
200 OK2017-12-29
200 OK2017-12-26
200 OK2017-12-22
200 OK2017-12-19
200 OK2017-12-15
200 OK2017-12-12
200 OK2017-12-08
200 OK2017-12-05
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200 OK2017-11-28
200 OK2017-11-24
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200 OK2017-11-17
200 OK2017-11-14
200 OK2017-11-10
200 OK2017-11-07
200 OK2017-11-03
200 OK2017-10-31
200 OK2017-10-27
200 OK2017-10-24
200 OK2017-10-20
200 OK2017-10-17
200 OK2017-10-13
200 OK2017-10-10
200 OK2017-10-06
200 OK2017-10-03
200 OK2017-09-29
200 OK2017-09-26
200 OK2017-09-22
200 OK2017-09-19
200 OK2017-09-15
200 OK2017-09-12
200 OK2017-09-08
200 OK2017-09-05
200 OK2017-09-01
200 OK2017-08-29
200 OK2017-08-25
200 OK2017-08-22
200 OK2017-08-18
200 OK2017-08-15
200 OK2017-08-11
200 OK2017-08-08
200 OK2017-08-04
200 OK2017-08-01
200 OK2017-07-28
200 OK2017-07-25
200 OK2017-07-21
200 OK2017-07-18
200 OK2017-07-14
200 OK2017-07-04
200 OK2017-06-30
200 OK2017-06-27
200 OK2017-06-23
200 OK2017-06-20
200 OK2017-06-16
200 OK2017-06-13
200 OK2017-06-09
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200 OK2017-06-02
200 OK2017-05-30
200 OK2017-05-26
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200 OK2017-05-19
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200 OK2017-03-14
200 OK2017-03-10
200 OK2017-03-07
200 OK2017-03-03
200 OK2017-02-28
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200 OK2017-02-17
200 OK2017-02-14
200 OK2017-02-10
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200 OK2016-08-09
200 OK2016-08-05
200 OK2016-08-02
200 OK2016-07-29
200 OK2016-07-26
200 OK2016-07-22
200 OK2016-07-19
200 OK2016-07-15
200 OK2016-07-12
200 OK2016-07-08
200 OK2016-07-05
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200 OK2016-06-17
200 OK2016-06-14
200 OK2016-06-10
200 OK2016-06-07
200 OK2016-06-03
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200 OK2016-05-17
200 OK2016-05-13
200 OK2016-05-10
200 OK2016-05-06
200 OK2016-05-03
200 OK2016-04-29
200 OK2016-04-26
200 OK2016-04-22
200 OK2016-04-19
200 OK2016-04-15
200 OK2016-04-12
200 OK2016-04-08
200 OK2016-04-05
200 OK2016-04-01
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200 OK2016-02-17
200 OK2016-02-15
200 OK2016-02-14
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200 OK2016-02-08
200 OK2016-02-07
200 OK2016-02-05
200 OK2016-02-03
200 OK2016-02-01
200 OK2016-01-31
200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
200 OK2016-01-22
200 OK2016-01-20
200 OK2016-01-18
200 OK2016-01-17
200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
200 OK2016-01-08
200 OK2016-01-06
200 OK2016-01-04

Tags

Protein
Eukaryota Prokaryote
protein domain protein family

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lina Ma [2016-08-17]
    • Lina Ma [2016-04-13]
    • Shixiang Sun [2016-03-28]
    • Shixiang Sun [2015-11-22]
    • Shixiang Sun [2015-06-28]
    • Shixiang Sun [2015-06-26]
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