The PROSITE database

By Nicolas Hulo, Amos Bairoch, Virginie Bulliard, L. Cerutti, Edouard De Castro, Petra S. Langendijk-Genevaux, M. Pagni, Christian J. A. Sigrist. Nucleic Acids Res., 2005

1,040 citations recorded by the source corpus.

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 .

Subfields: Cell Biology, Cellular and Molecular Neuroscience, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a0883d134b5abb7928483eb0859832a66a51fbf9

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cell Biology

Peer Bork

In Cellular and Molecular Neuroscience

In Molecular Biology

Citations in the corpus

Discovering Sequence Motifs with Arbitrary Insertions and Deletions (2008, neutral): “PROSITE is a database of protein motifs represented by either ‘‘patterns’’ (regular expressions) or ‘‘profiles’’ (hidden Markov models) [16].”
Molecular characterization of EgMYB1, a putative transcriptional repressor of the lignin biosynthetic pathway (2007, methodology): “Two putative domain functions were assigned by Prosite [33]: a N-myristoylation site (PS00008; starting position 6 of the motif) and a casein kinase II phosphorylation site (PS00006; starting position 10–13 of the motif).”
Spatial expression of transcription factors in Drosophila embryonic organ development (2013, methodology): “When available, we used the Pfam models [48] which for zf-C2H2 DBDs are more restrictive than the models used by other protein domain databases such as SMART [49] or Prosite [50].”
Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies (2009, background): “Databases of motifs [28–30], sequence profiles [31,32], and ortholog sets [33,34], are available for use in computational annotation.”
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins (2006, methodology): “ScanProsite provides a web interface to identify protein matches against signatures from the PROSITE database (2).”
The comprehensive microbial resource (2000, methodology): “Also available are evidence types associated with annotation such as HMMs (TIGRFAMs and Pfams), BLAST, InterPro (14), NCBI COG (15) and PROSITE (16), individual gene attributes and identifiers from other centers such as GenBank and Swiss-Prot/ UniProt (17), manually curated information on each genom”
New developments in the InterPro database (2007, methodology): “Reference InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER.”
Improved human disease candidate gene prioritization using mouse phenotype (2007, background): “[41], Pfam [42], SMART [43], PROSITE [44], Gene3D [45] and ProDom [46].”
LEA (Late Embryogenesis Abundant) proteins and their encoding genes in Arabidopsis thaliana (2008, background): “In the Prosite [ 124 ,125] database, two patterns defining dehydrins are present.”
Genome-wide analysis and identification of genes related to potassium transporter families in rice (Oryza sativa L.) (2007, neutral): “uk/InterProScan/) [38] and Pfam databases [39].”
Functional Knowledge Transfer for High-accuracy Prediction of Under-studied Biological Processes (2013, methodology): “Protein sequence similarity between genes was obtained from Biomart [82], and protein domain data were treated as binary evidence from PfamA [83] and Prosite [84].”
COBALT: constraint-based alignment tool for multiple protein sequences (2007, background): “…for further development in the field of multiple alignment: (1) The use of biologically relevant information encoded in databases such as the conserved domain database (Marchler-Bauer et al ., 2005) (CDD) and PROSITE (Hulo et al ., 2006) for improving the quality of multiple alignments.”
SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny (2008, neutral): “The InterPro consortium integrates databases of protein families, domains and functional sites, including: Gene3D (30), PANTHER (31), Pfam (32), PIRSF (33), PRINTS (34), ProDom (35), PROSITE (36), SMART (37), SUPERFAMILY and TIGRFAMs (38).”
Protein structure homology modeling using SWISS-MODEL workspace (2008, background): “database, a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families; ProfileScan—the target sequence is searched against the profiles collection of PROSIT”