{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T21:28:53Z","timestamp":1761514133284,"version":"3.37.3"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2018,1,10]],"date-time":"2018-01-10T00:00:00Z","timestamp":1515542400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"EPSRC","doi-asserted-by":"publisher","award":["EP\/I017909\/1"],"award-info":[{"award-number":["EP\/I017909\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"EPSRC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"MRC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009138","name":"CDT","doi-asserted-by":"publisher","award":["EP\/L016044\/1"],"award-info":[{"award-number":["EP\/L016044\/1"]}],"id":[{"id":"10.13039\/100009138","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"MRC","doi-asserted-by":"publisher","award":["G9722488"],"award-info":[{"award-number":["G9722488"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000163","name":"ARC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000163","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Hydrogen bonds (H-bonds) play an essential role for many molecular interactions but are also often transient, making visualising them in a flexible system challenging.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We provide pyHVis3D which allows for an easy to interpret 3D visualisation of H-bonds resulting from molecular simulations. We demonstrate the power of pyHVis3D by using it to explain the changes in experimentally measured binding affinities for three T-cell receptor\/peptide\/MHC complexes and mutants of each of these complexes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>pyHVis3D can be downloaded for free from http:\/\/opig.stats.ox.ac.uk\/resources.<\/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>","DOI":"10.1093\/bioinformatics\/btx842","type":"journal-article","created":{"date-parts":[[2018,1,9]],"date-time":"2018-01-09T17:28:11Z","timestamp":1515518891000},"page":"1941-1943","source":"Crossref","is-referenced-by-count":5,"title":["pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5714-7105","authenticated-orcid":false,"given":"Bernhard","family":"Knapp","sequence":"first","affiliation":[{"name":"Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, UK"},{"name":"Department of Basic Sciences, International University of Catalonia, Josep Trueta, s\/n 08195 Sant Cugat del Vall\u00e8s, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marta","family":"Alcala","sequence":"additional","affiliation":[{"name":"Department of Basic Sciences, International University of Catalonia, Josep Trueta, s\/n 08195 Sant Cugat del Vall\u00e8s, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hao","family":"Zhang","sequence":"additional","affiliation":[{"name":"Sir William Dunn School of Pathology, University of Oxford, S Parks Rd, Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Clare E","family":"West","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"P Anton","family":"van der Merwe","sequence":"additional","affiliation":[{"name":"Sir William Dunn School of Pathology, University of Oxford, S Parks Rd, Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Charlotte M","family":"Deane","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,1,10]]},"reference":[{"key":"2023012810011332400_btx842-B1","doi-asserted-by":"crossref","first-page":"2714","DOI":"10.1002\/elps.1150181505","article-title":"SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling","volume":"18","author":"Guex","year":"1997","journal-title":"Electrophoresis"},{"key":"2023012810011332400_btx842-B8","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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