{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T19:16:41Z","timestamp":1762543001278,"version":"3.37.3"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2019,2,15]],"date-time":"2019-02-15T00:00:00Z","timestamp":1550188800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100010198","name":"Ministerio de Econom\u00eda, Industria y Competitividad, Gobierno de Espa\u00f1a","doi-asserted-by":"publisher","award":["BIO2016-76400-R(AEI\/FEDER, UE)"],"award-info":[{"award-number":["BIO2016-76400-R(AEI\/FEDER, UE)"]}],"id":[{"id":"10.13039\/501100010198","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012818","name":"Comunidad de Madrid","doi-asserted-by":"publisher","award":["S2017\/BMD-3817"],"award-info":[{"award-number":["S2017\/BMD-3817"]}],"id":[{"id":"10.13039\/100012818","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","award":["PT13\/0001\/0009"],"award-info":[{"award-number":["PT13\/0001\/0009"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"name":"INB","award":["PT17\/0009\/0010 - ISCIII-SGEFI\/ERDF"],"award-info":[{"award-number":["PT17\/0009\/0010 - ISCIII-SGEFI\/ERDF"]}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020","doi-asserted-by":"publisher","award":["Elixir \u2013 EXCELERATE INFRADEV-3-2015, Proposal 676559","INFRAIA-1-2014-2015, Proposal 653706"],"award-info":[{"award-number":["Elixir \u2013 EXCELERATE INFRADEV-3-2015, Proposal 676559","INFRAIA-1-2014-2015, Proposal 653706"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Ministerio de Ciencia, Innovaci\u00f3n y Universidades, Gobierno de Espa\u00f1a","award":["E-28-2018-0015407"],"award-info":[{"award-number":["E-28-2018-0015407"]}]},{"DOI":"10.13039\/501100003176","name":"Ministerio de Educaci\u00f3n, Cultura y Deporte","doi-asserted-by":"publisher","award":["FPU-2015\/264"],"award-info":[{"award-number":["FPU-2015\/264"]}],"id":[{"id":"10.13039\/501100003176","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Many diseases are associated to single nucleotide polymorphisms that affect critical regions of proteins as binding sites or post translational modifications. Therefore, analysing genomic variants with structural and molecular biology data is a powerful framework in order to elucidate the potential causes of such diseases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>A new version of our web framework 3DBIONOTES is presented. This version offers new tools to analyse and visualize protein annotations and genomic variants, including a contingency analysis of variants and amino acid features by means of a Fisher exact test, the integration of a gene annotation viewer to highlight protein features on gene sequences and a protein\u2013protein interaction viewer to display protein annotations at network level.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The web server is available at https:\/\/3dbionotes.cnb.csic.es<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>Spanish National Institute for Bioinformatics (INB ELIXIR-ES) and Biocomputing Unit, National Centre of Biotechnology (CSIC)\/Instruct Image Processing Centre, C\/ Darwin n\u00ba 3, Campus of Cantoblanco, 28049 Madrid, Spain.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz118","type":"journal-article","created":{"date-parts":[[2019,2,15]],"date-time":"2019-02-15T14:14:14Z","timestamp":1550240054000},"page":"3512-3513","source":"Crossref","is-referenced-by-count":9,"title":["3DBIONOTES v3.0: crossing molecular and structural biology data with genomic variations"],"prefix":"10.1093","volume":"35","author":[{"given":"Joan","family":"Segura","sequence":"first","affiliation":[{"name":"Spanish National Institute for Bioinformatics (INB ELIXIR-ES) and Biocomputing Unit, National Centre of Biotechnology (CSIC)\/Instruct Image Processing Centre , Madrid, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6156-3542","authenticated-orcid":false,"given":"Ruben","family":"Sanchez-Garcia","sequence":"additional","affiliation":[{"name":"Spanish National Institute for Bioinformatics (INB ELIXIR-ES) and Biocomputing Unit, National Centre of Biotechnology (CSIC)\/Instruct Image Processing Centre , Madrid, Spain"}]},{"given":"C O S","family":"Sorzano","sequence":"additional","affiliation":[{"name":"Spanish National Institute for Bioinformatics (INB ELIXIR-ES) and Biocomputing Unit, National Centre of Biotechnology (CSIC)\/Instruct Image Processing Centre , Madrid, Spain"}]},{"given":"J M","family":"Carazo","sequence":"additional","affiliation":[{"name":"Spanish National Institute for Bioinformatics (INB ELIXIR-ES) and Biocomputing Unit, National Centre of Biotechnology (CSIC)\/Instruct Image Processing Centre , Madrid, Spain"}]}],"member":"286","published-online":{"date-parts":[[2019,2,15]]},"reference":[{"key":"2023013108051824800_btz118-B1","first-page":"D464","article-title":"RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy","volume-title":"Nucleic Acids Res","author":"Burley","year":"2018"},{"key":"2023013108051824800_btz118-B2","doi-asserted-by":"crossref","first-page":"D1128","DOI":"10.1093\/nar\/gkx907","article-title":"BioMuta and BioXpress: mutation and expression knowledgebases for cancer biomarker discovery","volume":"46","author":"Dingerdissen","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023013108051824800_btz118-B3","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1038\/nmeth.2289","article-title":"Interactome3D: adding structural details to protein networks","volume":"10","author":"Mosca","year":"2013","journal-title":"Nat. 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