{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T17:57:27Z","timestamp":1772042247367,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2021,9,3]],"date-time":"2021-09-03T00:00:00Z","timestamp":1630627200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["200020_165868"],"award-info":[{"award-number":["200020_165868"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["200020_192153"],"award-info":[{"award-number":["200020_192153"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006447","name":"University of Zurich","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006447","id-type":"DOI","asserted-by":"publisher"}]},{"name":"UZH Forschungskredit","award":["FK-17-098"],"award-info":[{"award-number":["FK-17-098"]}]},{"name":"University of Applied Sciences Mittweida"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Quantitative interpretation of single-molecule FRET experiments requires a model of the dye dynamics to link experimental energy transfer efficiencies to distances between atom positions. We have developed FRETraj, a Python module to predict FRET distributions based on accessible-contact volumes (ACV) and simulated photon statistics. FRETraj helps to identify optimal fluorophore positions on a biomolecule of interest by rapidly evaluating donor-acceptor distances. FRETraj is scalable and fully integrated into PyMOL and the Jupyter ecosystem. Here, we describe the conformational dynamics of a DNA hairpin by computing multiple ACVs along a molecular dynamics trajectory and compare the predicted FRET distribution with single-molecule experiments. FRET-assisted modeling will accelerate the analysis of structural ensembles in particular dynamic, non-coding RNAs and transient protein-nucleic acid complexes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>FRETraj is implemented as a cross-platform Python package available under the GPL-3.0 on Github (https:\/\/github.com\/RNA-FRETools\/fretraj) and is documented at https:\/\/RNA-FRETools.github.io\/fretraj.<\/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\/btab615","type":"journal-article","created":{"date-parts":[[2021,9,3]],"date-time":"2021-09-03T17:06:29Z","timestamp":1630688789000},"page":"3953-3955","source":"Crossref","is-referenced-by-count":15,"title":["FRETraj: integrating single-molecule spectroscopy with molecular dynamics"],"prefix":"10.1093","volume":"37","author":[{"given":"Fabio D","family":"Steffen","sequence":"first","affiliation":[{"name":"Department of Chemistry, University of Zurich , Zurich CH 8057, Switzerland"}]},{"given":"Roland K O","family":"Sigel","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Zurich , Zurich CH 8057, Switzerland"}]},{"given":"Richard","family":"B\u00f6rner","sequence":"additional","affiliation":[{"name":"Department of Chemistry, University of Zurich , Zurich CH 8057, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2021,9,3]]},"reference":[{"key":"2023051608163704600_btab615-B1","doi-asserted-by":"crossref","first-page":"2721","DOI":"10.1016\/j.bpj.2015.04.038","article-title":"Quantitative interpretation of FRET experiments via molecular simulation: force field and validation","volume":"108","author":"Best","year":"2015","journal-title":"Biophys. 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