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Database information

PROSITE (Database of protein domains, families and functional sites)

General information

Description: PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them
Year founded: 1988
Last update: 2018-05-23
Version: 2018_05
Accessibility:
Manual:
Accessible
Real time : Checking...
Country/Region: Switzerland
Data type:
Data object:
Database category:
Major organism:
NA
Keywords:

Contact information

University/Institution: Swiss Institute of Bioinformatics
Address: 1 rue Michel Servet, 1211 Geneva 4, Switzerland
City: Geneva
Province/State:
Country/Region: Switzerland
Contact name (PI/Team): Christian J. A. Sigrist
Contact email (PI/Helpdesk): prosite-group@isb-sib.ch

Related Database

Record metadata

Created on: 2015-06-20
Curated by:
Lina Ma [2018-06-07]
Shixiang Sun [2016-03-28]
Shixiang Sun [2015-11-22]
Shixiang Sun [2015-06-28]
Shixiang Sun [2015-06-26]

Ranking

All databases:
55/4548 (98.813%)
Gene genome and annotation:
27/1211 (97.853%)
55
Total Rank
4,534
Citations
156.345
z-index

Community reviews

Not Rated
Data quality & quantity:
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System accessibility & reliability:

Word cloud

Publications

23161676
New and continuing developments at PROSITE. [PMID: 23161676]
Sigrist CJ, de Castro E, Cerutti L, Cuche BA, Hulo N, Bridge A, Bougueleret L, Xenarios I.

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.

Nucleic Acids Res. 2013:41(Database issue) | 369 Citations (from Europe PMC, 2020-05-30)
19858104
PROSITE, a protein domain database for functional characterization and annotation. [PMID: 19858104]
Sigrist CJ, Cerutti L, de Castro E, Langendijk-Genevaux PS, Bulliard V, Bairoch A, Hulo N.

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/.

Nucleic Acids Res. 2010:38(Database issue) | 367 Citations (from Europe PMC, 2020-05-30)
18003654
The 20 years of PROSITE. [PMID: 18003654]
Hulo N, Bairoch A, Bulliard V, Cerutti L, Cuche BA, de Castro E, Lachaize C, Langendijk-Genevaux PS, Sigrist CJ.

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/.

Nucleic Acids Res. 2008:36(Database issue) | 232 Citations (from Europe PMC, 2020-05-30)
16381852
The PROSITE database. [PMID: 16381852]
Hulo N, Bairoch A, Bulliard V, Cerutti L, De Castro E, Langendijk-Genevaux PS, Pagni M, Sigrist CJ.

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/.

Nucleic Acids Res. 2006:34(Database issue) | 409 Citations (from Europe PMC, 2020-05-30)
14681377
Recent improvements to the PROSITE database. [PMID: 14681377]
Hulo N, Sigrist CJ, Le Saux V, Langendijk-Genevaux PS, Bordoli L, Gattiker A, De Castro E, Bucher P, Bairoch A.

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/.

Nucleic Acids Res. 2004:32(Database issue) | 203 Citations (from Europe PMC, 2020-05-30)
12230035
PROSITE: a documented database using patterns and profiles as motif descriptors. [PMID: 12230035]
Sigrist CJ, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P.

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.

Brief Bioinform. 2002:3(3) | 395 Citations (from Europe PMC, 2020-05-30)
11752303
The PROSITE database, its status in 2002. [PMID: 11752303]
Falquet L, Pagni M, Bucher P, Hulo N, Sigrist CJ, Hofmann K, Bairoch A.

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.

Nucleic Acids Res. 2002:30(1) | 594 Citations (from Europe PMC, 2020-05-30)
9847184
The PROSITE database, its status in 1999. [PMID: 9847184]
Hofmann K, Bucher P, Falquet L, Bairoch A.

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.

Nucleic Acids Res. 1999:27(1) | 576 Citations (from Europe PMC, 2020-05-30)
9016539
The PROSITE database, its status in 1997. [PMID: 9016539]
Bairoch A, Bucher P, Hofmann K.

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.

Nucleic Acids Res. 1997:25(1) | 435 Citations (from Europe PMC, 2020-05-30)
8594577
The PROSITE database, its status in 1995. [PMID: 8594577]
Bairoch A, Bucher P, Hofmann K.

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.

Nucleic Acids Res. 1996:24(1) | 125 Citations (from Europe PMC, 2020-05-30)
7937064
PROSITE: recent developments. [PMID: 7937064]
Bairoch A, Bucher P.

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.

Nucleic Acids Res. 1994:22(17) | 79 Citations (from Europe PMC, 2020-05-30)
8332530
The PROSITE dictionary of sites and patterns in proteins, its current status. [PMID: 8332530]
Bairoch A.
Nucleic Acids Res. 1993:21(13) | 192 Citations (from Europe PMC, 2020-05-30)
1598232
PROSITE: a dictionary of sites and patterns in proteins. [PMID: 1598232]
Bairoch A.
Nucleic Acids Res. 1992:20 Suppl() | 251 Citations (from Europe PMC, 2020-05-30)
2041810
PROSITE: a dictionary of sites and patterns in proteins. [PMID: 2041810]
Bairoch A.
Nucleic Acids Res. 1991:19 Suppl() | 307 Citations (from Europe PMC, 2020-05-30)