{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,6,22]],"date-time":"2023-06-22T21:14:54Z","timestamp":1687468494307},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"7","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Protein sequence and structure representation and manipulation require dedicated software libraries to support methods of increasing complexity. Here, we describe the VIrtual Constrution TOol for pRoteins (Victor) C++ library, an open source platform dedicated to enabling inexperienced users to develop advanced tools and gathering contributions from the community. The provided application examples cover statistical energy potentials, profile\u2013profile sequence alignments and ab initio loop modeling. Victor was used over the last 15 years in several publications and optimized for efficiency. It is provided as a GitHub repository with source files and unit tests, plus extensive online documentation, including a Wiki with help files and tutorials, examples and Doxygen documentation.<\/jats:p>\n               <jats:p>Availability and implementation: The C++ library and online documentation, distributed under a GPL license are available from URL: http:\/\/protein.bio.unipd.it\/victor\/.<\/jats:p>\n               <jats:p>Contact: \u00a0silvio.tosatto@unipd.it<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu773","type":"journal-article","created":{"date-parts":[[2014,11,21]],"date-time":"2014-11-21T01:18:58Z","timestamp":1416532738000},"page":"1138-1140","source":"Crossref","is-referenced-by-count":6,"title":["The Victor C++ library for protein representation and advanced manipulation"],"prefix":"10.1093","volume":"31","author":[{"given":"Layla","family":"Hirsh","sequence":"first","affiliation":[{"name":"1 Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, 2Department of Engineering, Pontificia Universidad Cat\u00f3lica del Per\u00fa, San Miguel, 32 Lima, Per\u00fa and 3Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy"},{"name":"1 Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, 2Department of Engineering, Pontificia Universidad Cat\u00f3lica del Per\u00fa, San Miguel, 32 Lima, Per\u00fa and 3Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Damiano","family":"Piovesan","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, 2Department of Engineering, Pontificia Universidad Cat\u00f3lica del Per\u00fa, San Miguel, 32 Lima, Per\u00fa and 3Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manuel","family":"Giollo","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, 2Department of Engineering, Pontificia Universidad Cat\u00f3lica del Per\u00fa, San Miguel, 32 Lima, Per\u00fa and 3Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy"},{"name":"1 Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, 2Department of Engineering, Pontificia Universidad Cat\u00f3lica del Per\u00fa, San Miguel, 32 Lima, Per\u00fa and 3Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carlo","family":"Ferrari","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, 2Department of Engineering, Pontificia Universidad Cat\u00f3lica del Per\u00fa, San Miguel, 32 Lima, Per\u00fa and 3Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Silvio C. E.","family":"Tosatto","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Sciences, University of Padua, Viale G. Colombo 3, 35131 Padova, Italy, 2Department of Engineering, Pontificia Universidad Cat\u00f3lica del Per\u00fa, San Miguel, 32 Lima, Per\u00fa and 3Department of Information Engineering, University of Padua, Via Gradenigo 6, 35121 Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2014,11,19]]},"reference":[{"key":"2023051309143618800_btu773-B1","doi-asserted-by":"crossref","first-page":"2626","DOI":"10.1093\/bioinformatics\/btq481","article-title":"OpenStructure: a flexible software framework for computational structural biology","volume":"26","author":"Biasini","year":"2010","journal-title":"Bioinformatics"},{"key":"2023051309143618800_btu773-B2","doi-asserted-by":"crossref","first-page":"2914","DOI":"10.1093\/bioinformatics\/bti438","article-title":"MollDE: a homology modeling framework you can click with","volume":"21","author":"Canutescu","year":"2005","journal-title":"Bioinformatics"},{"key":"2023051309143618800_btu773-B3","doi-asserted-by":"crossref","first-page":"2018","DOI":"10.1093\/bioinformatics\/btm269","article-title":"StrBioLib: a Java library for development of custom computational structural biology applications","volume":"23","author":"Chandonia","year":"2007","journal-title":"Bioinformatics"},{"key":"2023051309143618800_btu773-B4","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1093\/bioinformatics\/bti013","article-title":"The SSEA server for protein secondary structure alignment","volume":"21","author":"Fontana","year":"2005","journal-title":"Bioinformatics"},{"key":"2023051309143618800_btu773-B5","volume-title":"Design Patterns: Elements of Reusable Object-Oriented Software","author":"Gamma","year":"1995"},{"key":"2023051309143618800_btu773-B6","doi-asserted-by":"crossref","first-page":"S7","DOI":"10.1186\/1471-2164-15-S4-S7","article-title":"NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation","volume":"15","author":"Giollo","year":"2014","journal-title":"BMC Genomics"},{"key":"2023051309143618800_btu773-B7","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1093\/bioinformatics\/btl655","article-title":"Biskit\u2014a software platform for structural bioinformatics","volume":"23","author":"Gr\u00fcnberg","year":"2007","journal-title":"Bioinformatics"},{"key":"2023051309143618800_btu773-B8","doi-asserted-by":"crossref","first-page":"S162","DOI":"10.1002\/elps.200900140","article-title":"Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective","volume":"30","author":"Guex","year":"2009","journal-title":"Electrophoresis"},{"key":"2023051309143618800_btu773-B9","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1186\/1471-2105-11-531","article-title":"BALL\u2014biochemical algorithms library 1.3","volume":"11","author":"Hildebrandt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2023051309143618800_btu773-B10","doi-asserted-by":"crossref","first-page":"W478","DOI":"10.1093\/nar\/gku377","article-title":"Enhancing UCSF Chimera through web services","volume":"42","author":"Huang","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023051309143618800_btu773-B11","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. 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