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However, due to the impact of molecular flexibility, the performance of current methods has hit a bottleneck in realistic unbound docking. Pushing the limit, we have proposed a protein-ensemble\u2013RNA docking strategy to explicitly consider the protein flexibility in protein\u2013RNA docking through an ensemble of multiple protein structures, which is referred to as MPRDock. Instead of taking conformations from MD simulations or experimental structures, we obtained the multiple structures of a protein by building models from its homologous templates in the Protein Data Bank (PDB).<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Our approach can not only avoid the reliability issue of structures from MD simulations but also circumvent the limited number of experimental structures for a target protein in the PDB. Tested on 68 unbound\u2013bound and 18 unbound\u2013unbound protein\u2013RNA complexes, our MPRDock\/DITScorePR considerably improved the docking performance and achieved a significantly higher success rate than single-protein rigid docking whether pseudo-unbound templates are included or not. Similar improvements were also observed when combining our ensemble docking strategy with other scoring functions. The present homology model-based ensemble docking approach will have a general application in molecular docking for other interactions.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>http:\/\/huanglab.phys.hust.edu.cn\/mprdock\/<\/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\/btz388","type":"journal-article","created":{"date-parts":[[2019,5,3]],"date-time":"2019-05-03T19:17:47Z","timestamp":1556911067000},"page":"4994-5002","source":"Crossref","is-referenced-by-count":24,"title":["Protein-ensemble\u2013RNA docking by efficient consideration of protein flexibility through homology models"],"prefix":"10.1093","volume":"35","author":[{"given":"Jiahua","family":"He","sequence":"first","affiliation":[{"name":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology , Wuhan, Hubei, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huanyu","family":"Tao","sequence":"additional","affiliation":[{"name":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology , Wuhan, Hubei, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sheng-You","family":"Huang","sequence":"additional","affiliation":[{"name":"Institute of Biophysics, School of Physics, Huazhong University of Science and Technology , Wuhan, Hubei, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,5,14]]},"reference":[{"key":"2023013108321037800_btz388-B1","doi-asserted-by":"crossref","first-page":"2271","DOI":"10.1016\/j.bpj.2018.02.038","article-title":"Ensemble docking in drug discovery","volume":"114","author":"Amaro","year":"2018","journal-title":"Biophys. 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