{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:59Z","timestamp":1772138039763,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2020,7,19]],"date-time":"2020-07-19T00:00:00Z","timestamp":1595116800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/L018756\/1"],"award-info":[{"award-number":["BB\/L018756\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/M026280\/1"],"award-info":[{"award-number":["BB\/M026280\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UK Catalysis Hub [Engineering and Physical Sciences Research Council","award":["EP\/M013219\/1"],"award-info":[{"award-number":["EP\/M013219\/1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Experimental structural data can allow detailed insight into protein structure and protein\u2013ligand interactions, which is crucial for many areas of bioscience, including drug design and enzyme engineering. Typically, however, little more than a static picture of protein\u2013ligand interactions is obtained, whereas dynamical information is often required for deeper understanding and to assess the effect of mutations. Molecular dynamics (MD) simulations can provide such information, but setting up and running these simulations is not straightforward and requires expert knowledge. There is thus a need for a tool that makes protein\u2013ligand simulation easily accessible to non-expert users.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present Enlighten2: efficient simulation protocols for protein\u2013ligand systems alongside a user-friendly plugin to the popular visualization program PyMOL. With Enlighten2, non-expert users can straightforwardly run and visualize MD simulations on protein\u2013ligand models of interest. There is no need to learn new programs and all underlying tools are free and open source.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The Enlighten2 Python package and PyMOL plugin are free to use under the GPL3.0 licence and can be found at https:\/\/enlighten2.github.io. We also provide a lightweight Docker image via DockerHub that includes Enlighten2 with all the required utilities.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa643","type":"journal-article","created":{"date-parts":[[2020,7,14]],"date-time":"2020-07-14T15:09:47Z","timestamp":1594739387000},"page":"5104-5106","source":"Crossref","is-referenced-by-count":14,"title":["Enlighten2: molecular dynamics simulations of protein\u2013ligand systems made accessible"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1052-5698","authenticated-orcid":false,"given":"Kirill","family":"Zinovjev","sequence":"first","affiliation":[{"name":"School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk , Bristol BS8 1TD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8060-3359","authenticated-orcid":false,"given":"Marc W","family":"van der Kamp","sequence":"additional","affiliation":[{"name":"School of Biochemistry, University of Bristol, Biomedical Sciences Building, University Walk , Bristol BS8 1TD, UK"}]}],"member":"286","published-online":{"date-parts":[[2020,7,19]]},"reference":[{"key":"2023062408113652000_btaa643-B1","doi-asserted-by":"crossref","first-page":"6095","DOI":"10.1021\/jacs.6b00232","article-title":"The catalytic mechanism of a natural Diels\u2013Alderase revealed in molecular detail","volume":"138","author":"Byrne","year":"2016","journal-title":"J. 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