ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins

By Edouard De Castro, Christian J. A. Sigrist, Alexandre Gattiker, Virginie Bulliard, Petra S. Langendijk-Genevaux, Elisabeth Gasteiger, Amos Bairoch, Nicolas Hulo. Nucleic Acids Res., 2006

1,658 citations recorded by the source corpus.

ScanProsite——is a new and improved version of the web-based tool for detecting PROSITE signature matches in protein sequences. For a number of PROSITE profiles, the tool now makes use of ProRules—context-dependent annotation templates—to detect functional and structural intra-domain residues. The detection of those features enhances the power of function prediction based on profiles. Both user-defined sequences and sequences from the UniProt Knowledgebase can be matched against custom patterns, or against PROSITE signatures. To improve response times, matches of sequences from UniProtKB against PROSITE signatures are now retrieved from a pre-computed match database. Several output modes are available including simple text views and a rich mode providing an interactive match and feature viewer with a graphical representation of results.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a6f0c509d0c9482a8b5affa6116cbf23b7c7c17f

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Citations in the corpus

Current challenges and best-practice protocols for microbiome analysis (2019, positive): “Databases like PROSITE [131], PRINTS [132], or InterPro are utilized to screen common motifs in metagenomic sequences.”
The EMBL-EBI search and sequence analysis tools APIs in 2019 (2019, background): “Tools such as PromoterWise (19) and Wise2DBA (20) along with ScanProsite (21), MAFFT addseq (22) and RaXML-EPA (23) have been retired.”
CAMPR3: a database on sequences, structures and signatures of antimicrobial peptides (2015, methodology): “The generated patterns and HMMs were queried against the protein database of NCBI and UniProtKB using ScanProsite tool (19) and jackhmmer tool of HMMER web server (20), respectively, to retrieve hits.”
New and continuing developments at PROSITE (2012, neutral): “org/ scanprosite/) allows users to search protein sequences against all PROSITE signatures, and to search for matches to defined PROSITE signatures in the UniProtKB and PDB databases (4).”
Molecular Cloning of Dormancy-associated MADS-box Gene Homologs and Their Characterization during Seasonal Endodormancy Transitional Phases of Japanese Pear (2010, methodology): “ScanProsite: Detection of PROSITE signature matches and ProRuleassociated functional and structural residues in proteins.”
Transmembrane Membrane Readers form a Novel Class of Proteins That Include Peripheral Phosphoinositide Recognition Domains and Viral Spikes (2022, neutral): “Protein sequences were obtained from UniProt [19].”