The 20 years of PROSITE
Nucleic Acids Res., 2007
537 citations recorded by the source corpus.
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/.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/c06e4c4c7e750dbb29b3358ea9ead5fbbb2f7387
Citations in the corpus
- PDBe: Protein Data Bank in Europe (2010, background): “org/), GO (18), PROSITE (19) and UniProt (12) databases for the selected enzyme class.”
- Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical–gene–disease networks (2008, background): “Protein sequence pages (associated with a Gene page) are, in turn, additionally linked to records from GenPept (14), InterPro (37), PRINTS (38), PROSITE (39), ProDom (40), SMART (41), Pfam (42) and, when appropriate, to a species-specific gene page in FlyBase (43) or ZFIN (44).”
- Hidden Markov Models and their Applications in Biological Sequence Analysis (2009, background): “Currently, we have two such libraries that have compiled a large number of profile-HMMs for various protein families: the PROSITE database [36, 37] and the Pfam database [38, 39].”
- ELM—the database of eukaryotic linear motifs (2011, background): “Several resources are devoted to the annotation and/or detection of SLiMs [Prosite (10), MiniMotifMiner (11) and Scansite (12)].”
- New and continuing developments at PROSITE (2012, methodology): “We used this information to perform a restricted search of the murine proteome using a degenerate pattern corresponding to the two iron-coordinating histidines of aromatic amino acid hydroxylase (H–”
- A comprehensive review and comparison of different computational methods for protein remote homology detection (2018, methodology): “Besides, several profile HMM resources have been built for HMM alignment, such as the PROSITE database [55, 56] and the Pfam database [22].”
- Linear Motif Atlas for Phosphorylation-Dependent Signaling (2008, methodology): “[RK] is commonly used to search for cyclin-dependent kinase (CDK) substrates ( 14 , 18 , 19 ).”