What is PROSITE?
Database of protein domains, families and functional sites. PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them [More... / References / Commercial users ].
What is the difference between motifs and profiles in PROSITE?
The motif descriptors used in PROSITE are either patterns or profiles, which are derived from multiple alignments of homologous sequences. PROSITE patterns are short sequence motifs, while PROSITE profiles are position specific score matrices. Profiles characterize protein domains over their entire length, and they are more sensitive than patterns.
How can PROSITE help in improving the functional characterization of domains?
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.
What information can I find from a PROSITE signature?
Each PROSITE signature is linked to an annotation document where the user can find information on the protein family or domain detected by the signature, such as the origin of its name, taxonomic occurrence, domain architecture, function, 3D structure, main characteristics of the sequence, domain size and literature references (1).
What is PROSITE used for?
PROSITE, a protein domain database for functional characterization and annotation. PROSITE's uses include identifying possible functions of newly discovered proteins and analysis of known proteins for previously undetermined activity.
What are PROSITE patterns?
PROSITE patterns are short sequence motifs, while PROSITE profiles are position specific score matrices. Profiles characterize protein domains over their entire length, and they are more sensitive than patterns. Profiles and patterns have complementary qualities.
Is PROSITE a secondary database?
PROSITE and PRINTS are the only manually annotated secondary databases. The print is a diagnostic collection of protein fingerprints.
What is Expasy PROSITE?
PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. This resource supports COVID-19 / SARS-CoV-2 research. Developed by the Swiss-Prot group and supported by the SIB Swiss Institute of Bioinformatics.
How do you reference a PROSITE?
If you want to refer to the PROSITE methodology please cite: Sigrist C.J.A., Cerutti L., Hulo N., Gattiker A., Falquet L., Pagni M., Bairoch A., Bucher P. PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform.
What is the difference between Cath and SCOP?
These domains are classified in a hierarchical manner: SCOP sorts protein domains into classes, folds, superfamilies and families while the four major levels of CATH are class, architecture, topology and homologous superfamily.
What is Cath in bioinformatics?
The CATH database[3,4] is a classification of protein domains (sub-sequences of proteins that may fold, evolve and function independently of the rest of the protein), based not only on sequence information, but also on structural and functional properties.
What is PDB in bioinformatics?
Protein Data Bank (PDB) is the single worldwide archive of structural data of biological macromolecules. It includes data obtained by X-ray crystallography and nuclear magnetic resonance (NMR) spectrometry submitted by biologists and biochemists from all over the world.
What is Swiss-Prot database?
SWISS-PROT (1) is an annotated protein sequence database, which was created at the Department of Medical Biochemistry of the University of Geneva and has been a collaborative effort of the Department and the European Molecular Biology Laboratory (EMBL), since 1987.
What is TrEMBL?
Introduction TrEMBL is a computer-annotated protein sequence database supplementing the SWISS-PROT Protein Sequence Data Bank. TrEMBL contains the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database not yet integrated in SWISS-PROT.
What is Expasy translation?
Translate is a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence.
What is motif in Bioinformatics?
In Bioinformatics, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and has been proven or assumed to have a biological significance.
What is a protete?
PROSITE is an annotated collection of motif descriptors dedicated to the identification of protein families and domains. The motif descriptors used in PROSITE are either patterns or profiles, which are derived from multiple alignments of homologous sequences. PROSITE patterns are short sequence motifs, while PROSITE profiles are position specific score matrices. Profiles characterize protein domains over their entire length, and they are more sensitive than patterns. Profiles and patterns have complementary qualities. Patterns, confined to small regions with high sequence similarity, are often powerful predictors of protein functions such as enzymatic activities. Profiles covering complete domains are more suitable for predicting protein structural properties.
What is Swiss 2DPAGE?
The SWISS-2DPAGE is a fully implemented 2-DE federated database. The ExPASy WWW server is home to five locally maintained databases (SWISS-PROT, SWISS-2DPAGE, PROSITE, SWISS-3DIMAGE and ENZYME). Besides the database service, the server offers special tools for proteomic analysis, such as PeptIdent for peptide mass fingerprinting. SWISS-PROT serves as a searchable main index, prepared according to rule 3, and has cross-references to the other four databases. SWISS-2DPAGE contains data on protein identified on various 2-D PAGE reference maps. The hypertext cross-references as of 15 June 1999 include links to SWISS-PROT, YPD database of yeast Saccharomyces and the ECO2DBASE E. coli database. The X-ray crystallography Protein Data Bank (PDB), the Mendelian Inheritance in Man data bank (OMIM), the G-protein-coupled receptor database (GCRDb) and the database of yeast ( Saccharomyces cerevisiae) genes coding for proteins (LISTA) are also linked through SWISS-PROT.
Is Entrez the be all and end all source of protein sequence information?
Although Entrez might appear to be the be-all and end-all source of protein and nucleotide sequence information, this is not quite true. There are many smaller but well curated databases of biologic information that are not included among the databases that Entrez serves. These include the Prosite and Blocks databases of protein structural motifs, transcription factor databases, species-specific databases, and databases devoted to certain pathogens.
What is a protein?
PROSITE is a database of protein families and domains. It is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor.
What is a protein signature?
Similarly, a protein signature can be used to assign a newly sequenced protein to a specific family of proteins and thus to formulate hypotheses about its function. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains.
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