PROSITE, a protein domain database for functional characterization and annotation

By Christian J. A. Sigrist, L. Cerutti, Edouard De Castro, Petra S. Langendijk-Genevaux, Virginie Bulliard, Amos Bairoch, Nicolas Hulo. 2009

567 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 these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE is largely used for the annotation of domain features of UniProtKB/Swiss-Prot entries. Among the 983 (DNA-binding) domains, repeats and zinc fingers present in Swiss-Prot (release 57.8 of 22 September 2009), 696 (∼70%) are annotated with PROSITE descriptors using information from ProRule. 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. Here, we describe AMSA, an annotated multiple sequence alignment format used to build a new generation of generalized profiles, the migration of ScanProsite to Vital-IT, a cluster of 633 CPUs, and the adoption of the Distributed Annotation System (DAS) to facilitate PROSITE data integration and interchange with other sources. The latest version of PROSITE (release 20.54, of 22 September 2009) contains 1308 patterns, 863 profiles and 869 ProRules. PROSITE is accessible at: http://www.expasy.org/prosite/.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability (2013, neutral): “There already exist databases of carefully aligned and annotated sequences (Cole et al. 2009; Sigrist et al. 2010; Punta et al. 2012), in which each MSA consists of a small number (typically up to (cid:2) 1,000) of sequences.”
Better prediction of functional effects for sequence variants (2015, neutral): “Additionally, we introduced new features for SNAP2: amino acid properties as provided by the AAindex database [42], predicted binding residues [43], predicted disordered regions [44], proximity to N- and C-terminus, statistical contact potentials [45], co-evolving positions, residue annotations from”
The Pfam protein families database (2011, positive): “Further information was extracted from the Pfam database and added to the infobox, such as the Pfam clan accession and links to other database sites such as PROSITE (10), SCOP (11) and CAZy (12).”
How Common Is Disorder? Occurrence of Disordered Residues in Four Domains of Life (2015, unknown): “To this end, several databases are currently available: PROSITE, InterPro, Pfam, and ModiDP [1–4].”
InterPro in 2011: new developments in the family and domain prediction database (2011, unknown): “The InterPro database integrates predictive models, or signatures, from multiple, diverse source repositories: Pfam (1), PRINTS (2), PROSITE (3), SMART (4), ProDom (5), PIRSF (6), SUPERFAMILY (7), PANTHER (8), CATHGene3D (9), TIGRFAMs (10) and HAMAP (11).”
Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal (2012, unknown): “For this purpose the DeepView function “scan for Prosite Patterns” (85) of the “Edit” menu can be applied.”
New and continuing developments at PROSITE (2012, unknown): “Since our last report in the NAR database issue (6), PROSITE has increased the number of available signatures to 1308 patterns and 1039 profiles, which are associated with 1041 ProRules and 1650 documentation entries.”
3D deep convolutional neural networks for amino acid environment similarity analysis (2017, unknown): “Figure 8b shows a microenvironment surrounding a PROSITE [58] INSULIN motif [59], with the key CYS residue removed (PDB:1IZA [60], CYS 7.)”
MuSiC: Identifying mutational significance in cancer genomes (2012, unknown): “(Patternscan is a new version of the Prosite database [Sigrist et al. 2010].)”
A comprehensive review and comparison of different computational methods for protein remote homology detection (2018, unknown): “Besides, several profile HMM resources have been built for HMM alignment, such as the PROSITE database [55, 56] and the Pfam database [22].”