PROSITE
Encyclopedia
PROSITE is a protein database. It consists of entries describing the protein families, domains and functional sites as well as amino acid
patterns, signatures, and profiles in them. These are manually curated by a team of the Swiss Institute of Bioinformatics
and tightly integrated into Swiss-Prot protein annotation. PROSITE was created in 1988 by Amos Bairoch
, who directed the group for more than 20 years. Since July 2009 the director of the PROSITE, Swiss-Prot and Vital-IT groups is Ioannis Xenarios.
PROSITE's uses include identifying possible functions of newly discovered proteins and analysis of known proteins for previously undetermined activity. Properties from well-studied gene
s can be propagated to biologically related organisms, and for different or poorly known genes biochemical functions can be predicted from similarities. PROSITE offers tools for protein sequence analysis
and motif detection (see sequence motif
, PROSITE patterns). It is part of the ExPASy
proteomics
analysis servers.
The database ProRule builds on the domain descriptions of PROSITE. It provides additional information about functionally or structurally critical amino acids. The rules contain information about biologically meaningful residues, like active sites, substrate
- or co-factor
-binding sites, posttranslational modification sites or disulfide
bonds, to help function determination. These can automatically generate annotation based on PROSITE motifs.
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
patterns, signatures, and profiles in them. These are manually curated by a team of the Swiss Institute of Bioinformatics
Swiss Institute of Bioinformatics
The Swiss Institute of Bioinformatics is an academic not-for-profit foundation which federates bioinformatics activities throughout Switzerland...
and tightly integrated into Swiss-Prot protein annotation. PROSITE was created in 1988 by Amos Bairoch
Amos Bairoch
Amos Bairoch is a Swiss bioinformatician, born 22 November 1957.Bairoch is currently professor of Bioinformatics at the Department of Structural biology and Bioinformatics of the University of Geneva and group leader at the Swiss Institute of Bioinformatics...
, who directed the group for more than 20 years. Since July 2009 the director of the PROSITE, Swiss-Prot and Vital-IT groups is Ioannis Xenarios.
PROSITE's uses include identifying possible functions of newly discovered proteins and analysis of known proteins for previously undetermined activity. Properties from well-studied gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
s can be propagated to biologically related organisms, and for different or poorly known genes biochemical functions can be predicted from similarities. PROSITE offers tools for protein sequence analysis
Sequence analysis
In bioinformatics, the term sequence analysis refers to the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. Methodologies used include sequence alignment, searches against biological...
and motif detection (see sequence motif
Sequence motif
In genetics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has, or is conjectured to have, a biological significance...
, PROSITE patterns). It is part of the ExPASy
ExPASy
ExPASy is a bioinformatics resource portal operated by the Swiss Institute of Bioinformatics and in particular the SIB Web Team. It is an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences...
proteomics
Proteomics
Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
analysis servers.
The database ProRule builds on the domain descriptions of PROSITE. It provides additional information about functionally or structurally critical amino acids. The rules contain information about biologically meaningful residues, like active sites, substrate
Substrate (biochemistry)
In biochemistry, a substrate is a molecule upon which an enzyme acts. Enzymes catalyze chemical reactions involving the substrate. In the case of a single substrate, the substrate binds with the enzyme active site, and an enzyme-substrate complex is formed. The substrate is transformed into one or...
- or co-factor
Cofactor (biochemistry)
A cofactor is a non-protein chemical compound that is bound to a protein and is required for the protein's biological activity. These proteins are commonly enzymes, and cofactors can be considered "helper molecules" that assist in biochemical transformations....
-binding sites, posttranslational modification sites or disulfide
Disulfide
In chemistry, a disulfide usually refers to the structural unit composed of a linked pair of sulfur atoms. Disulfide usually refer to a chemical compound that contains a disulfide bond, such as diphenyl disulfide, C6H5S-SC6H5....
bonds, to help function determination. These can automatically generate annotation based on PROSITE motifs.
See also
- UniprotUniProtUniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many of which are derived from genome sequencing projects...
the universal protein database, a central resource on protein information - PROSITE adds data to it. - InterProInterProInterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them....
a centralized database, grouping data from databases of protein families, domains and functional sites - part of the data come from PROSITE. - Protein subcellular localization predictionProtein subcellular localization predictionProtein subcellular localization prediction involves the computational prediction of where a protein resides in a cell. Prediction of protein subcellular localization is an important component of bioinformatics-based prediction of protein function and genome annotation, and it can aid the...
another example of use of PROSITE.