{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T20:01:02Z","timestamp":1761163262840,"version":"build-2065373602"},"reference-count":31,"publisher":"Wiley","issue":"8","license":[{"start":{"date-parts":[[2015,3,3]],"date-time":"2015-03-03T00:00:00Z","timestamp":1425340800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"name":"FWO-Vlaanderen","award":["3G037510"],"award-info":[{"award-number":["3G037510"]}]},{"name":"Ghent University"},{"name":"BOF12\/GOA\/014"}],"content-domain":{"domain":["analyticalsciencejournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Proteomics"],"published-print":{"date-parts":[[2015,4]]},"abstract":"<jats:p>\n                    The integration of a protein's structure with its known sequence variation provides insight on how that protein evolves, for instance in terms of (changing) function or immunogenicity. Yet, collating the corresponding sequence variants into a multiple sequence alignment, calculating each position's conservation, and mapping this information back onto a relevant structure is not straightforward. We therefore built the Sequence Conservation on Protein 3D structure (\n                    <jats:italic>scop3D<\/jats:italic>\n                    ) tool to perform these tasks automatically. The output consists of two modified PDB files in which the\n                    <jats:italic>B<\/jats:italic>\n                    \u2010values for each position are replaced by the percentage sequence conservation, or the information entropy for each position, respectively. Furthermore, text files with absolute and relative amino acid occurrences for each position are also provided, along with snapshots of the protein from six distinct directions in space. The visualization provided by\n                    <jats:italic>scop3D<\/jats:italic>\n                    can for instance be used as an aid in vaccine development or to identify antigenic hotspots, which we here demonstrate based on an analysis of the fusion proteins of human respiratory syncytial virus and mumps virus.\n                  <\/jats:p>","DOI":"10.1002\/pmic.201400354","type":"journal-article","created":{"date-parts":[[2015,1,31]],"date-time":"2015-01-31T05:24:01Z","timestamp":1422681841000},"page":"1448-1452","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Scop3D: Three\u2010dimensional visualization of sequence conservation"],"prefix":"10.1002","volume":"15","author":[{"given":"Tessa","family":"Vermeire","sequence":"first","affiliation":[{"name":"Department of Medical Protein Research VIB  Ghent Belgium"},{"name":"Department of Biochemistry Ghent University  Ghent Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Stijn","family":"Vermaere","sequence":"additional","affiliation":[{"name":"Department of Medical Protein Research VIB  Ghent Belgium"},{"name":"Department of Biochemistry Ghent University  Ghent Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bert","family":"Schepens","sequence":"additional","affiliation":[{"name":"VIB Inflammation Research Center  Ghent Belgium"},{"name":"Department of Biomedical Molecular Biology Ghent University  Ghent Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xavier","family":"Saelens","sequence":"additional","affiliation":[{"name":"VIB Inflammation Research Center  Ghent Belgium"},{"name":"Department of Biomedical Molecular Biology Ghent University  Ghent Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Steven","family":"Van Gucht","sequence":"additional","affiliation":[{"name":"Viral Diseases Communicable and Infectious Diseases Scientific Institute of Public Health (WIV\u2010ISP)  Elsene Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lennart","family":"Martens","sequence":"additional","affiliation":[{"name":"Department of Medical Protein Research VIB  Ghent Belgium"},{"name":"Department of Biochemistry Ghent University  Ghent Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Elien","family":"Vandermarliere","sequence":"additional","affiliation":[{"name":"Department of Medical Protein Research VIB  Ghent Belgium"},{"name":"Department of Biochemistry Ghent University  Ghent Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2015,3,3]]},"reference":[{"key":"e_1_2_5_2_1","doi-asserted-by":"publisher","DOI":"10.1038\/181662a0"},{"key":"e_1_2_5_3_1","first-page":"2","volume-title":"Protein Structure and Function","author":"Petsko G. 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