{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T21:47:20Z","timestamp":1770068840752,"version":"3.49.0"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2021,5,17]],"date-time":"2021-05-17T00:00:00Z","timestamp":1621209600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35GM138146"],"award-info":[{"award-number":["R35GM138146"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["IIS2030722"],"award-info":[{"award-number":["IIS2030722"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI1942692"],"award-info":[{"award-number":["DBI1942692"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The DeepRefiner webserver, freely available at http:\/\/watson.cse.eng.auburn.edu\/DeepRefiner\/, is an interactive and fully configurable online system for high-accuracy protein structure refinement. Fuelled by deep learning, DeepRefiner offers the ability to leverage cutting-edge deep neural network architectures which can be calibrated for on-demand selection of adventurous or conservative refinement modes targeted at degree or consistency of refinement. The method has been extensively tested in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiments under the group name \u2018Bhattacharya-Server\u2019 and was officially ranked as the No. 2 refinement server in CASP13 (second only to \u2018Seok-server\u2019 and outperforming all other refinement servers) and No. 2 refinement server in CASP14 (second only to \u2018FEIG-S\u2019 and outperforming all other refinement servers including \u2018Seok-server\u2019). The DeepRefiner web interface offers a number of convenient features, including (i) fully customizable refinement job submission and validation; (ii) automated job status update, tracking, and notifications; (ii) interactive and interpretable web-based results retrieval with quantitative and visual analysis and (iv) extensive help information on job submission and results interpretation via web-based tutorial and help tooltips.<\/jats:p>","DOI":"10.1093\/nar\/gkab361","type":"journal-article","created":{"date-parts":[[2021,4,23]],"date-time":"2021-04-23T19:14:09Z","timestamp":1619205249000},"page":"W147-W152","source":"Crossref","is-referenced-by-count":37,"title":["DeepRefiner: high-accuracy protein structure refinement by deep network calibration"],"prefix":"10.1093","volume":"49","author":[{"given":"Md Hossain","family":"Shuvo","sequence":"first","affiliation":[{"name":"Department of Computer Science and Software Engineering, Auburn University, Auburn, AL 36849, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Muhammad","family":"Gulfam","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Software Engineering, Auburn University, Auburn, AL 36849, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9630-0141","authenticated-orcid":false,"given":"Debswapna","family":"Bhattacharya","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Software Engineering, Auburn University, Auburn, AL 36849, USA"},{"name":"Department of Biological Sciences, Auburn University, Auburn, AL 36849, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,5,17]]},"reference":[{"key":"2021070812075821800_B1","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1038\/s41586-019-1923-7","article-title":"Improved protein structure prediction using potentials from deep learning","volume":"577","author":"Senior","year":"2020","journal-title":"Nature"},{"key":"2021070812075821800_B2","doi-asserted-by":"crossref","first-page":"1496","DOI":"10.1073\/pnas.1914677117","article-title":"Improved protein structure prediction using predicted interresidue orientations","volume":"117","author":"Yang","year":"2020","journal-title":"Proc. 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