New and continuing developments at PROSITE

By Christian J. A. Sigrist, Edouard De Castro, L. Cerutti, Béatrice A. Cuche, Nicolas Hulo, A. Bridge, L. Bougueleret, Ioannis Xenarios. Nucleic Acids Res., 2012

1,517 citations recorded by the source corpus.

PROSITE (http://prosite.expasy.org/) 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, which increases the discriminatory power of these profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. PROSITE signatures, together with ProRule, are used for the annotation of domains and features of UniProtKB/Swiss-Prot entries. Here, we describe recent developments that allow users to perform whole-proteome annotation as well as a number of filtering options that can be combined to perform powerful targeted searches for biological discovery. The latest version of PROSITE (release 20.85, of 30 August 2012) contains 1308 patterns, 1039 profiles and 1041 ProRules.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/5728a2594f19babf8c796ea7e93c035a0153f8ad

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Citations in the corpus

PredictProtein—an open resource for online prediction of protein structural and functional features (2014, positive): “In addition, functional motifs are taken from PROSITE (13) and domains from Pfam (14).”
The InterPro protein families and domains database: 20 years on (2020, background): “InterPro integrates 13 protein signature databases into one central resource: CATH-Gene3D (1), the Conserved Domains Database (CDD) (2), HAMAP (3), PANTHER (4), Pfam (5), PIRSF (6), PRINTS (7), PROSITE Patterns (8), PROSITE Profiles (8), SMART (9), the Structure–Function Linkage Database (SFLD) (10)”
InterPro in 2019: improving coverage, classification and access to protein sequence annotations (2018, methodology): “Launched in 1999, InterPro is derived from 14 different specialist member databases: CATH-Gene3D (2), the Conserved Do-mains Database (CDD) (3), HAMAP (4), PANTHER (5), Pfam (6), PIRSF (7), PRINTS (8), ProDom (9), PROSITE Patterns (10), PROSITE Profiles (10), SMART (11), the Structure–Function Linka”
Defining the human C2H2 zinc-finger degrome targeted by thalidomide analogs through CRBN (2018, methodology): “3A) highlighted shared residues that are part of the PROSITE C2H2 ZF search motif (IKZF3 C148, C151, H164, H168, and F155), residues that stabilize the ternary fold of the ZF domain (IKZF3 L161), and residues that frequently appear within C2H2 ZF domains (IKZF3 G152).”
InterProScan 5: genome-scale protein function classification (2014, methodology): “As InterProScan 5 makes use of the Hibernate object-relational mapping tool (http://www.hibernate.org/), it should be possible to port the back-end to run on most relational database management systems.”
Genome-wide identification and characterization of the aquaporin gene family in Sorghum bicolor (L.) (2015, methodology): “All remaining protein sequences were examined using the domain analysis program PROSITE with default cutoff parameters (Sigrist et al., 2013).”
Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome. (2017, neutral): “0 Phytpzome; (Rensing et al., 2008) http://genome.jgi.doe.gov Spirogyra pratensis transcriptome (Ju et al., 2015) https://www.ncbi.nlm.nih.gov/Traces/wgs/ wgsviewer.cgi?val=GBSM01&search= GBSM01000000&display=scaffolds Coleochaete orbicularis transcriptome (Ju et al., 2015) https://www.ncbi.nlm.nih.”
InterPro in 2017—beyond protein family and domain annotations (2016, background): “The signatures are provided by 14 different member databases: 12 of these are long-standing members of the InterPro Consortium (CATH-Gene3D (3), HAMAP (4), PANTHER (5), Pfam (6), PIRSF (7), PRINTS (8), ProDom (9), PROSITE Patterns (10), PROSITE Profiles (10), SMART (11), SUPERFAMILY (12) and TIGRFAM”
The Papillomavirus Episteme: a major update to the papillomavirus sequence database (2016, methodology): “PROSITE protein-motif database (33) to define a collection of pairwise constraints.”
The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases (2015, background): “…(unreviewed and automatically annotated) makes extensive use of expert-curated resources from SIB such as PROSITE (http://prosite.expasy.org) (25) and HAMAP (http://hamap. expasy.org) (26), which are both available as web-based resources for external users to annotate their own protein and…”
IBS: an illustrator for the presentation and visualization of biological sequences (2015, methodology): “The first attempt at providing a professional illustrator of MyDomains for biological sequences was made by the PROSITE database (Sigrist et al. , 2013).”