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It can be used to identify active compounds and reveal molecular mechanisms of biological processes. A successful docking usually requires thorough conformation sampling and scoring, which are computationally expensive and difficult. Recent studies demonstrated that it can be beneficial to docking with the guidance of existing similar co-crystal structures. In this work, we developed a protein\u2013ligand docking method, named FitDock, which fits initial conformation to the given template using a hierarchical multi-feature alignment approach, subsequently explores the possible conformations and finally outputs refined docking poses. In our comprehensive benchmark tests, FitDock showed 40%\u201360% improvement in terms of docking success rate and an order of magnitude faster over popular docking methods, if template structures exist (&amp;gt; 0.5 ligand similarity). FitDock has been implemented in a user-friendly program, which could serve as a convenient tool for drug design and molecular mechanism exploration. It is now freely available for academic users at http:\/\/cao.labshare.cn\/fitdock\/.<\/jats:p>","DOI":"10.1093\/bib\/bbac087","type":"journal-article","created":{"date-parts":[[2022,2,21]],"date-time":"2022-02-21T12:08:34Z","timestamp":1645445314000},"source":"Crossref","is-referenced-by-count":254,"title":["FitDock: protein\u2013ligand docking by template fitting"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0027-3861","authenticated-orcid":false,"given":"Xiaocong","family":"Yang","sequence":"first","affiliation":[{"name":"Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2517-9436","authenticated-orcid":false,"given":"Yang","family":"Liu","sequence":"additional","affiliation":[{"name":"Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China"}]},{"given":"Jianhong","family":"Gan","sequence":"additional","affiliation":[{"name":"Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China"}]},{"given":"Zhi-Xiong","family":"Xiao","sequence":"additional","affiliation":[{"name":"Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1925-2123","authenticated-orcid":false,"given":"Yang","family":"Cao","sequence":"additional","affiliation":[{"name":"Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China"},{"name":"Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China"}]}],"member":"286","published-online":{"date-parts":[[2022,3,14]]},"reference":[{"key":"2022051813453558100_ref1","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1007\/s10822-006-9060-4","article-title":"Development and validation of a modular, extensible docking program: DOCK 5","volume":"20","author":"Moustakas","year":"2006","journal-title":"J Comput Aided Mol Des"},{"key":"2022051813453558100_ref2","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1006\/jmbi.1996.0477","article-title":"A fast flexible docking method using an incremental construction algorithm","volume":"261","author":"Rarey","year":"1996","journal-title":"J Mol Biol"},{"key":"2022051813453558100_ref3","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1023\/A:1007913026166","article-title":"Multiple automatic base selection: protein\u2013ligand docking based on incremental construction without manual intervention","volume":"11","author":"Rarey","year":"1997","journal-title":"J Comput Aided Mol Des"},{"key":"2022051813453558100_ref4","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1002\/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B","article-title":"Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function","volume":"19","author":"Morris","year":"1998","journal-title":"J Comput Chem"},{"key":"2022051813453558100_ref5","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1006\/jmbi.1996.0897","article-title":"Development and validation of a genetic algorithm for flexible docking","volume":"267","author":"Gareth","year":"1997","journal-title":"J Mol Biol"},{"key":"2022051813453558100_ref6","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1002\/prot.10465","article-title":"Improved protein-ligand docking using GOLD","volume":"52","author":"Verdonk","year":"2003","journal-title":"Proteins"},{"key":"2022051813453558100_ref7","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1021\/jm0306430","article-title":"Glide: a new approach for rapid, accurate docking and scoring. 1. 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