{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T07:40:08Z","timestamp":1762674008077},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":571,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The interpretation of cancer-related single-nucleotide variants (SNVs) considering the protein features they affect, such as known functional sites, protein\u2013protein interfaces, or relation with already annotated mutations, might complement the annotation of genetic variants in the analysis of NGS data. Current tools that annotate mutations fall short on several aspects, including the ability to use protein structure information or the interpretation of mutations in protein complexes.<\/jats:p>\n               <jats:p>Results: We present the Structure\u2013PPi system for the comprehensive analysis of coding SNVs based on 3D protein structures of protein complexes. The 3D repository used, Interactome3D, includes experimental and modeled structures for proteins and protein\u2013protein complexes. Structure\u2013PPi annotates SNVs with features extracted from UniProt, InterPro, APPRIS, dbNSFP and COSMIC databases. We illustrate the usefulness of Structure\u2013PPi with the interpretation of 1\u2009027\u2009122 non-synonymous SNVs from COSMIC and the 1000G Project that provides a collection of \u223c172 700 SNVs mapped onto the protein 3D structure of 8726 human proteins (43.2% of the 20\u2009214 SwissProt-curated proteins in UniProtKB release 2014_06) and protein\u2013protein interfaces with potential functional implications.<\/jats:p>\n               <jats:p>Availability and implementation: Structure\u2013PPi, along with a user manual and examples, isavailable at http:\/\/structureppi.bioinfo.cnio.es\/Structure, the code for local installations at https:\/\/github.com\/Rbbt-Workflows<\/jats:p>\n               <jats:p>Contact: \u00a0tpons@cnio.es<\/jats:p>\n               <jats:p>Supplementary Information \u00a0: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv142","type":"journal-article","created":{"date-parts":[[2015,3,13]],"date-time":"2015-03-13T00:41:57Z","timestamp":1426207317000},"page":"2397-2399","source":"Crossref","is-referenced-by-count":36,"title":["Structure-PPi: a module for the annotation of cancer-related single-nucleotide variants at protein\u2013protein interfaces"],"prefix":"10.1093","volume":"31","author":[{"given":"Miguel","family":"V\u00e1zquez","sequence":"first","affiliation":[{"name":"Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain"}]},{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[{"name":"Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain"}]},{"given":"Tirso","family":"Pons","sequence":"additional","affiliation":[{"name":"Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain"}]}],"member":"286","published-online":{"date-parts":[[2015,3,11]]},"reference":[{"key":"2023020202154207300_btv142-B1","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nmeth0410-248","article-title":"A method and server for predicting damaging missense mutations","volume":"7","author":"Adzhubei","year":"2010","journal-title":"Nat. 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