{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T09:28:05Z","timestamp":1740130085775,"version":"3.37.3"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T00:00:00Z","timestamp":1558483200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31670724","31570722"],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2016YFC1305800","2016YFC1305805"],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2018KFYYXJJ033"],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003397","name":"Huazhong University of Science and Technology","doi-asserted-by":"publisher","award":["3004012104"],"id":[{"id":"10.13039\/501100003397","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,7,2]]},"abstract":"Abstract<\/jats:title>Interactions between nuclide acids (RNA\/DNA) play important roles in many basic cellular activities like transcription regulation, RNA processing, and protein synthesis. Therefore, determining the complex structures between RNAs\/DNAs is crucial to understand the molecular mechanism of related RNA\/DNA\u2013RNA\/DNA interactions. Here, we have presented HNADOCK, a user-friendly web server for nucleic acid (NA)\u2013nucleic acid docking to model the 3D complex structures between two RNAs\/DNAs, where both sequence and structure inputs are accepted for RNAs, while only structure inputs are supported for DNAs. HNADOCK server was tested through both unbound structure and sequence inputs on the benchmark of 60 RNA\u2013RNA complexes and compared with the state-of-the-art algorithm SimRNA. For structure input, HNADOCK server achieved a high success rate of 71.7% for top 10 predictions, compared to 58.3% for SimRNA. For sequence input, HNADOCK server also obtained a satisfactory performance and gave a success rate of 83.3% when the bound RNA templates are included or 53.3% when excluding those bound RNA templates. It was also found that inclusion of the inter-RNA base-pairing information from RNA\u2013RNA interaction prediction can significantly improve the docking accuracy, especially for the top prediction. HNADOCK is fast and can normally finish a job in about 10 minutes. The HNADOCK web server is available at http:\/\/huanglab.phys.hust.edu.cn\/hnadock\/.<\/jats:p>","DOI":"10.1093\/nar\/gkz412","type":"journal-article","created":{"date-parts":[[2019,5,6]],"date-time":"2019-05-06T15:33:52Z","timestamp":1557156832000},"page":"W35-W42","source":"Crossref","is-referenced-by-count":32,"title":["HNADOCK: a nucleic acid docking server for modeling RNA\/DNA\u2013RNA\/DNA 3D complex structures"],"prefix":"10.1093","volume":"47","author":[{"given":"Jiahua","family":"He","sequence":"first","affiliation":[{"name":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China"}]},{"given":"Jun","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China"}]},{"given":"Huanyu","family":"Tao","sequence":"additional","affiliation":[{"name":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China"}]},{"given":"Yi","family":"Xiao","sequence":"additional","affiliation":[{"name":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. China"}]},{"given":"Sheng-You","family":"Huang","sequence":"additional","affiliation":[{"name":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, P.R. 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