PHOSIDA


21081558	PHOSIDA 2011: the posttranslational modification database. [PMID: 21081558] Gnad F, Gunawardena J, Mann M. Abstract The primary purpose of PHOSIDA (http://www.phosida.com) is to manage posttranslational modification sites of various species ranging from bacteria to human. Since its last report, PHOSIDA has grown significantly in size and evolved in scope. It comprises more than 80,000 phosphorylated, N-glycosylated or acetylated sites from nine different species. All sites are obtained from high-resolution mass spectrometric data using the same stringent quality criteria. One of the main distinguishing features of PHOSIDA is the provision of a wide range of analysis tools. PHOSIDA is comprised of three main components: the database environment, the prediction platform and the toolkit section. The database environment integrates and combines high-resolution proteomic data with multiple annotations. High-accuracy species-specific phosphorylation and acetylation site predictors, trained on the modification sites contained in PHOSIDA, allow the in silico determination of modified sites on any protein on the basis of the primary sequence. The toolkit section contains methods that search for sequence motif matches or identify de novo consensus, sequences from large scale data sets. Nucleic Acids Res. 2011:39(Database issue) \| 249 Citations (from Europe PMC, 2025-03-15)
18039369	PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. [PMID: 18039369] Gnad F, Ren S, Cox J, Olsen JV, Macek B, Oroshi M, Mann M. Abstract PHOSIDA http://www.phosida.com, a phosphorylation site database, integrates thousands of high-confidence in vivo phosphosites identified by mass spectrometry-based proteomics in various species. For each phosphosite, PHOSIDA lists matching kinase motifs, predicted secondary structures, conservation patterns, and its dynamic regulation upon stimulus. Using support vector machines, PHOSIDA also predicts phosphosites. Genome Biol. 2007:8(11) \| 312 Citations (from Europe PMC, 2025-03-15)

PHOSIDA 2011: the posttranslational modification database. [PMID: 21081558]

Gnad F, Gunawardena J, Mann M.

The primary purpose of PHOSIDA (http://www.phosida.com) is to manage posttranslational modification sites of various species ranging from bacteria to human. Since its last report, PHOSIDA has grown significantly in size and evolved in scope. It comprises more than 80,000 phosphorylated, N-glycosylated or acetylated sites from nine different species. All sites are obtained from high-resolution mass spectrometric data using the same stringent quality criteria. One of the main distinguishing features of PHOSIDA is the provision of a wide range of analysis tools. PHOSIDA is comprised of three main components: the database environment, the prediction platform and the toolkit section. The database environment integrates and combines high-resolution proteomic data with multiple annotations. High-accuracy species-specific phosphorylation and acetylation site predictors, trained on the modification sites contained in PHOSIDA, allow the in silico determination of modified sites on any protein on the basis of the primary sequence. The toolkit section contains methods that search for sequence motif matches or identify de novo consensus, sequences from large scale data sets.

Nucleic Acids Res. 2011:39(Database issue) | 249 Citations (from Europe PMC, 2025-03-15)

PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. [PMID: 18039369]

Gnad F, Ren S, Cox J, Olsen JV, Macek B, Oroshi M, Mann M.

Abstract

PHOSIDA http://www.phosida.com, a phosphorylation site database, integrates thousands of high-confidence in vivo phosphosites identified by mass spectrometry-based proteomics in various species. For each phosphosite, PHOSIDA lists matching kinase motifs, predicted secondary structures, conservation patterns, and its dynamic regulation upon stimulus. Using support vector machines, PHOSIDA also predicts phosphosites.

Genome Biol. 2007:8(11) | 312 Citations (from Europe PMC, 2025-03-15)

URL:	http://www.phosida.com/
Full name:	phosphorylation site database
Description:	Phosida allows the retrieval of phosphorylation, acetylation, and N-glycosylation data of any protein of interest. It lists posttranslational modification sites associated with particular projects and proteomes or, alternatively, displays posttranslational modifications found for any protein or protein group of interest. In addition, structural and evolutionary information on each modified protein and posttranslational modification site is integrated.
Year founded:	2007
Last update:	2012-5-25
Version:	v1.0
Accessibility:	Accessible
Country/Region:	Germany

Data type:	Protein
Data object:	Animal Bacteria Fungi
Database category:	Modification
Major species:	Bacillus subtilis Caenorhabditis elegans Drosophila melanogaster Escherichia coli Halobacterium salinarum Homo sapiens Lactococcus lactis Mus musculus Saccharomyces cerevisiae
Keywords:	posttranslational modification site structural and evolutionary information

University/Institution:	Max Planck Institute of Biochemistry
Address:	Am Klopferspitz 18, D-82152 Martinsried, Germany
City:	Martinsried
Province/State:
Country/Region:	Germany
Contact name (PI/Team):	Matthias Mann
Contact email (PI/Helpdesk):	mmann@biochem.mpg.de

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Database Commons a catalog of worldwide biological databases