{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T09:02:41Z","timestamp":1769763761164,"version":"3.49.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2017,11,8]],"date-time":"2017-11-08T00:00:00Z","timestamp":1510099200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 GM084953 and R01 GM103695"],"award-info":[{"award-number":["R01 GM084953 and R01 GM103695"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Refinement of protein structure models is a long-standing problem in structural bioinformatics. Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global structure accuracy over other state-of-the-art servers.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PREFMD is freely available as a web server at http:\/\/feiglab.org\/prefmd. Scripts for running PREFMD as a stand-alone package are available at https:\/\/github.com\/feiglab\/prefmd.git.<\/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\/btx726","type":"journal-article","created":{"date-parts":[[2017,11,7]],"date-time":"2017-11-07T12:11:44Z","timestamp":1510056704000},"page":"1063-1065","source":"Crossref","is-referenced-by-count":38,"title":["PREFMD: a web server for protein structure refinement via molecular dynamics simulations"],"prefix":"10.1093","volume":"34","author":[{"given":"Lim","family":"Heo","sequence":"first","affiliation":[{"name":"Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9380-6422","authenticated-orcid":false,"given":"Michael","family":"Feig","sequence":"additional","affiliation":[{"name":"Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,11,8]]},"reference":[{"key":"2023012712480187000_btx726-B1","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1002\/jcc.21287","article-title":"CHARMM: the biomolecular simulation program","volume":"30","author":"Brooks","year":"2009","journal-title":"J. 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