{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,8]],"date-time":"2024-07-08T08:28:41Z","timestamp":1720427321210},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2018,1,27]],"date-time":"2018-01-27T00:00:00Z","timestamp":1517011200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R33-GM078601 and R01-GM100701"],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,6,1]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n Accurately mapping and annotating genomic locations on 3D protein structures is a key step in structure-based analysis of genomic variants detected by recent large-scale sequencing efforts. There are several mapping resources currently available, but none of them provides a web API (Application Programming Interface) that supports programmatic access.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n We present G2S, a real-time web API that provides automated mapping of genomic variants on 3D protein structures. G2S can align genomic locations of variants, protein locations, or protein sequences to protein structures and retrieve the mapped residues from structures. G2S API uses REST-inspired design and it can be used by various clients such as web browsers, command terminals, programming languages and other bioinformatics tools for bringing 3D structures into genomic variant analysis.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n The webserver and source codes are freely available at https:\/\/g2s.genomenexus.org.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty047","type":"journal-article","created":{"date-parts":[[2018,1,26]],"date-time":"2018-01-26T20:10:38Z","timestamp":1516997438000},"page":"1949-1950","source":"Crossref","is-referenced-by-count":11,"title":["G2S: a web-service for annotating genomic variants on 3D protein structures"],"prefix":"10.1093","volume":"34","author":[{"given":"Juexin","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Electrical Engineering & Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA"}]},{"given":"Robert","family":"Sheridan","sequence":"additional","affiliation":[{"name":"Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA"}]},{"given":"S Onur","family":"Sumer","sequence":"additional","affiliation":[{"name":"Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA"}]},{"given":"Nikolaus","family":"Schultz","sequence":"additional","affiliation":[{"name":"Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA"},{"name":"Department of Epidemiology-Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA"}]},{"given":"Dong","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering & Computer Science and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-5739-1781","authenticated-orcid":false,"given":"Jianjiong","family":"Gao","sequence":"additional","affiliation":[{"name":"Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,1,27]]},"reference":[{"key":"2023012713564147400_bty047-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023012713564147400_bty047-B2","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"Auton","year":"2015","journal-title":"Nature"},{"key":"2023012713564147400_bty047-B3","doi-asserted-by":"crossref","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","author":"Bateman","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023012713564147400_bty047-B4","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023012713564147400_bty047-B5","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1158\/2159-8290.CD-12-0095","article-title":"The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data","volume":"2","author":"Cerami","year":"2012","journal-title":"Cancer Discov"},{"key":"2023012713564147400_bty047-B6","doi-asserted-by":"crossref","first-page":"pl1","DOI":"10.1126\/scisignal.2004088","article-title":"Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal","volume":"6","author":"Gao","year":"2013","journal-title":"Sci. Signal"},{"key":"2023012713564147400_bty047-B7","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1186\/s13073-016-0393-x","article-title":"3D clusters of somatic mutations in cancer reveal numerous rare mutations as functional targets","volume":"9","author":"Gao","year":"2017","journal-title":"Genome Med"},{"key":"2023012713564147400_bty047-B8","doi-asserted-by":"crossref","first-page":"2096","DOI":"10.1093\/bioinformatics\/btn397","article-title":"BioJava: an open-source framework for bioinformatics","volume":"24","author":"Holland","year":"2008","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023012713564147400_bty047-B9","doi-asserted-by":"crossref","first-page":"3833","DOI":"10.1093\/bioinformatics\/btw547","article-title":"Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank","volume":"32","author":"Prlic","year":"2016","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023012713564147400_bty047-B10","doi-asserted-by":"crossref","first-page":"681","DOI":"10.1186\/s12864-016-3028-0","article-title":"G23D: online tool for mapping and visualization of genomic variants on 3D protein structures","volume":"17","author":"Solomon","year":"2016","journal-title":"BMC Genomics"},{"key":"2023012713564147400_bty047-B11","doi-asserted-by":"crossref","first-page":"D483","DOI":"10.1093\/nar\/gks1258","article-title":"SIFTS: Structure Integration with Function, Taxonomy and Sequences resource","volume":"41","author":"Velankar","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023012713564147400_bty047-B12","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1038\/ng.2764","article-title":"The Cancer Genome Atlas Pan-Cancer analysis project","volume":"45","author":"Weinstein","year":"2013","journal-title":"Nat. Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/11\/1949\/48937821\/bioinformatics_34_11_1949.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/11\/1949\/48937821\/bioinformatics_34_11_1949.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T14:28:50Z","timestamp":1674829730000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/11\/1949\/4827683"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,1,27]]},"references-count":12,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2018,6,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty047","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,6,1]]},"published":{"date-parts":[[2018,1,27]]}}}