{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:56Z","timestamp":1740185156055,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2022,5,5]],"date-time":"2022-05-05T00:00:00Z","timestamp":1651708800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Laboratory Directed Research and Development Program at Oak Ridge National Laboratory"},{"DOI":"10.13039\/100016818","name":"UT-Battelle, LLC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100016818","id-type":"DOI","asserted-by":"publisher"}]},{"name":"U.S. Department of Energy (DOE","award":["DE-AC05-00OR22725"],"award-info":[{"award-number":["DE-AC05-00OR22725"]}]},{"name":"Genomic Science program within the US Department of Energy Office of Science","award":["ERKP917"],"award-info":[{"award-number":["ERKP917"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,6,13]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>Easy-to-use, open-source, general-purpose programs for modeling a protein structure from inter-atomic distances are needed for modeling from experimental data and refinement of predicted protein structures. OpenMDlr is an open-source Python package for modeling protein structures from pairwise distances between any atoms, and optionally, dihedral angles. We provide a user-friendly input format for harnessing modern biomolecular force fields in an easy-to-install package that can efficiently make use of multiple compute cores.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and Implementation<\/jats:title><jats:p>OpenMDlr is available at https:\/\/github.com\/BSDExabio\/OpenMDlr-amber. The package is written in Python (versions 3.x). All dependencies are open-source and can be installed with the Conda package management system.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac307","type":"journal-article","created":{"date-parts":[[2022,4,29]],"date-time":"2022-04-29T19:22:02Z","timestamp":1651260122000},"page":"3297-3298","source":"Crossref","is-referenced-by-count":0,"title":["OpenMDlr: parallel, open-source tools for general protein structure modeling and refinement from pairwise distances"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2364-4039","authenticated-orcid":false,"given":"Russell B","family":"Davidson","sequence":"first","affiliation":[{"name":"Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, TN 37830, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jess","family":"Woods","sequence":"additional","affiliation":[{"name":"Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, TN 37830, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"T Chad","family":"Effler","sequence":"additional","affiliation":[{"name":"Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, TN 37830, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mathialakan","family":"Thavappiragasam","sequence":"additional","affiliation":[{"name":"Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, TN 37830, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5031-7343","authenticated-orcid":false,"given":"Julie C","family":"Mitchell","sequence":"additional","affiliation":[{"name":"Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, TN 37830, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3103-9333","authenticated-orcid":false,"given":"Jerry M","family":"Parks","sequence":"additional","affiliation":[{"name":"Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, TN 37830, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8233-3057","authenticated-orcid":false,"given":"Ada","family":"Sedova","sequence":"additional","affiliation":[{"name":"Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, TN 37830, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,5,5]]},"reference":[{"key":"2023041408192595900_","doi-asserted-by":"crossref","first-page":"2728","DOI":"10.1038\/nprot.2007.406","article-title":"Version 1.2 of the crystallography and NMR system","volume":"2","author":"Brunger","year":"2007","journal-title":"Nat. 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