{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,1]],"date-time":"2026-02-01T10:21:28Z","timestamp":1769941288597,"version":"3.49.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2017,9,26]],"date-time":"2017-09-26T00:00:00Z","timestamp":1506384000000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31670724"],"award-info":[{"award-number":["31670724"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003397","name":"Huazhong University of Science and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003397","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>With the discovery of more and more noncoding RNAs and their versatile functions, RNA\u2013RNA interactions have received increased attention. Therefore, determination of their complex structures is valuable to understand the molecular mechanism of the interactions. Given the high cost of experimental methods, computational approaches like molecular docking have played an important role in the determination of complex structures, in which a benchmark is critical for the development of docking algorithms.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Meeting the need, we have developed the first comprehensive and nonredundant RNA\u2013RNA docking benchmark (RRDB). The diverse dataset of 123 targets consists of 78 unbound-unbound and 45 bound-unbound (or unbound-bound) test cases. The dataset was classified into three groups according to the interface conformational changes between bound and unbound structures: 47 \u2018easy\u2019, 38 \u2018medium\u2019 and 38 \u2018difficult\u2019 targets. A docking test with the benchmark using ZDOCK 2.1 demonstrated the challenging nature of the RNA\u2013RNA docking problem and the important value of the present benchmark. The bound and unbound cases of the benchmark will be beneficial for the development and optimization of docking and scoring algorithms for RNA\u2013RNA interactions.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The benchmark is available at http:\/\/huanglab.phys.hust.edu.cn\/RRDbenchmark\/.<\/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\/btx615","type":"journal-article","created":{"date-parts":[[2017,9,23]],"date-time":"2017-09-23T11:09:15Z","timestamp":1506164955000},"page":"453-458","source":"Crossref","is-referenced-by-count":9,"title":["RRDB: a comprehensive and non-redundant benchmark for RNA\u2013RNA docking and scoring"],"prefix":"10.1093","volume":"34","author":[{"given":"Yumeng","family":"Yan","sequence":"first","affiliation":[{"name":"School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, People\u2019s Republic of China"}]},{"given":"Sheng-You","family":"Huang","sequence":"additional","affiliation":[{"name":"School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei, People\u2019s Republic of China"}]}],"member":"286","published-online":{"date-parts":[[2017,9,25]]},"reference":[{"key":"2023012712270133000_btx615-B1","doi-asserted-by":"crossref","first-page":"1866","DOI":"10.1002\/prot.24083","article-title":"A protein-RNA docking benchmark (I): nonredundant cases","volume":"80","author":"Barik","year":"2012","journal-title":"Proteins"},{"key":"2023012712270133000_btx615-B2","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1016\/S0006-3495(92)81649-1","article-title":"The nucleic acid database. 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