{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T14:42:03Z","timestamp":1774536123942,"version":"3.50.1"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2019,6,7]],"date-time":"2019-06-07T00:00:00Z","timestamp":1559865600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31100522"],"award-info":[{"award-number":["31100522"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National High Technology Research and Development Program of China","award":["2012AA020402"],"award-info":[{"award-number":["2012AA020402"]}]},{"name":"Special Program for Applied Research on Super Computation of the NSFC-Guangdong Joint Fund","award":["U1501501"],"award-info":[{"award-number":["U1501501"]}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2016YXMS017"],"award-info":[{"award-number":["2016YXMS017"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The main function of protein\u2013RNA interaction is to regulate the expression of genes. Therefore, studying protein\u2013RNA interactions is of great significance. The information of three-dimensional (3D) structures reveals that atomic interactions are particularly important. The calculation method for modeling a 3D structure of a complex mainly includes two strategies: free docking and template-based docking. These two methods are complementary in protein\u2013protein docking. Therefore, integrating these two methods may improve the prediction accuracy.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this article, we compare the difference between the free docking and the template-based algorithm. Then we show the complementarity of these two methods. Based on the analysis of the calculation results, the transition point is confirmed and used to integrate two docking algorithms to develop P3DOCK. P3DOCK holds the advantages of both algorithms. The results of the three docking benchmarks show that P3DOCK is better than those two non-hybrid docking algorithms. The success rate of P3DOCK is also higher (3\u201320%) than state-of-the-art hybrid and non-hybrid methods. Finally, the hierarchical clustering algorithm is utilized to cluster the P3DOCK\u2019s decoys. The clustering algorithm improves the success rate of P3DOCK. For ease of use, we provide a P3DOCK webserver, which can be accessed at www.rnabinding.com\/P3DOCK\/P3DOCK.html. An integrated protein\u2013RNA docking benchmark can be downloaded from http:\/\/rnabinding.com\/P3DOCK\/benchmark.html.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>www.rnabinding.com\/P3DOCK\/P3DOCK.html.<\/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\/btz478","type":"journal-article","created":{"date-parts":[[2019,6,4]],"date-time":"2019-06-04T11:40:34Z","timestamp":1559648434000},"page":"96-103","source":"Crossref","is-referenced-by-count":29,"title":["P3DOCK: a protein\u2013RNA docking webserver based on template-based and template-free docking"],"prefix":"10.1093","volume":"36","author":[{"given":"Jinfang","family":"Zheng","sequence":"first","affiliation":[{"name":"School of Physics, Huazhong University of Science and Technology , Wuhan, Hubei 430074, China"}]},{"given":"Xu","family":"Hong","sequence":"additional","affiliation":[{"name":"School of Physics, Huazhong University of Science and Technology , Wuhan, Hubei 430074, China"}]},{"given":"Juan","family":"Xie","sequence":"additional","affiliation":[{"name":"School of Physics, Huazhong University of Science and Technology , Wuhan, Hubei 430074, China"}]},{"given":"Xiaoxue","family":"Tong","sequence":"additional","affiliation":[{"name":"School of Physics, Huazhong University of Science and Technology , Wuhan, Hubei 430074, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7986-5178","authenticated-orcid":false,"given":"Shiyong","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Physics, Huazhong University of Science and Technology , Wuhan, Hubei 430074, China"}]}],"member":"286","published-online":{"date-parts":[[2019,6,7]]},"reference":[{"key":"2023013109500106100_btz478-B1","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1016\/j.jmb.2003.07.006","article-title":"The relationship between sequence and interaction divergence in proteins","volume":"332","author":"Aloy","year":"2003","journal-title":"J. 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