{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,17]],"date-time":"2026-04-17T08:42:17Z","timestamp":1776415337486,"version":"3.51.2"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,5,25]],"date-time":"2022-05-25T00:00:00Z","timestamp":1653436800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81973243"],"award-info":[{"award-number":["81973243"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Protein-ligand blind docking is a powerful method for exploring the binding sites of receptors and the corresponding binding poses of ligands. It has seen wide applications in pharmaceutical and biological researches. Previously, we proposed a blind docking server, CB-Dock, which has been under heavy use (over 200 submissions per day) by researchers worldwide since 2019. Here, we substantially improved the docking method by combining CB-Dock with our template-based docking engine to enhance the accuracy in binding site identification and binding pose prediction. In the benchmark tests, it yielded the success rate of \u223c85% for binding pose prediction (RMSD\u00a0&amp;lt;\u00a02.0 \u00c5), which outperformed original CB-Dock and most popular blind docking tools. This updated docking server, named CB-Dock2, reconfigured the input and output web interfaces, together with a highly automatic docking pipeline, making it a particularly efficient and easy-to-use tool for the bioinformatics and cheminformatics communities. The web server is freely available at https:\/\/cadd.labshare.cn\/cb-dock2\/.<\/jats:p>","DOI":"10.1093\/nar\/gkac394","type":"journal-article","created":{"date-parts":[[2022,5,5]],"date-time":"2022-05-05T20:09:12Z","timestamp":1651781352000},"page":"W159-W164","source":"Crossref","is-referenced-by-count":1524,"title":["CB-Dock2: improved protein\u2013ligand blind docking by integrating cavity detection, docking and homologous template fitting"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2517-9436","authenticated-orcid":false,"given":"Yang","family":"Liu","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\/0000-0003-0027-3861","authenticated-orcid":false,"given":"Xiaocong","family":"Yang","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":"Shuang","family":"Chen","sequence":"additional","affiliation":[{"name":"Chengdu Institute of Biology, Chinese Academy of Sciences , 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":[[2022,5,24]]},"reference":[{"key":"2022070500014990400_B1","doi-asserted-by":"crossref","first-page":"W443","DOI":"10.1093\/nar\/gkv315","article-title":"PLIP: fully automated protein\u2013ligand interaction profiler","volume":"43","author":"Salentin","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2022070500014990400_B2","doi-asserted-by":"crossref","first-page":"2149","DOI":"10.1093\/bioinformatics\/btn409","article-title":"Protein-ligand interaction prediction: an improved chemogenomics approach","volume":"24","author":"Jacob","year":"2008","journal-title":"Bioinformatics"},{"key":"2022070500014990400_B3","doi-asserted-by":"crossref","first-page":"15451","DOI":"10.1038\/s41598-017-15571-7","article-title":"Protein-ligand blind docking using QuickVina-W with inter-process spatio-temporal integration","volume":"7","author":"Hassan","year":"2017","journal-title":"Sci. Rep."},{"key":"2022070500014990400_B4","doi-asserted-by":"crossref","first-page":"1729","DOI":"10.1110\/ps.0202302","article-title":"Efficient docking of peptides to proteins without prior knowledge of the binding site","volume":"11","author":"Het\u00e9nyi","year":"2009","journal-title":"Protein Sci."},{"key":"2022070500014990400_B5","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1038\/s41586-021-03828-1","article-title":"Highly accurate protein structure prediction for the human proteome","volume":"596","author":"Tunyasuvunakool","year":"2021","journal-title":"Nature"},{"key":"2022070500014990400_B6","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1126\/science.abj8754","article-title":"Accurate prediction of protein structures and interactions using a three-track neural network","volume":"373","author":"Baek","year":"2021","journal-title":"Science"},{"key":"2022070500014990400_B7","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1038\/nrd3478","article-title":"Trends in the exploitation of novel drug targets","volume":"10","author":"Rask-Andersen","year":"2011","journal-title":"Nat. Rev. Drug Discov."},{"key":"2022070500014990400_B8","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1016\/j.drudis.2016.09.010","article-title":"Identification and validation of novel drug targets in mycobacterium tuberculosis","volume":"22","author":"Singh","year":"2017","journal-title":"Drug Discov. Today"},{"key":"2022070500014990400_B9","doi-asserted-by":"crossref","first-page":"W270","DOI":"10.1093\/nar\/gkr366","article-title":"SwissDock, a protein-small molecule docking web service based on EADock DSS","volume":"39","author":"Grosdidier","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2022070500014990400_B10","doi-asserted-by":"crossref","first-page":"W438","DOI":"10.1093\/nar\/gky439","article-title":"COACH-D: improved protein\u2013ligand binding sites prediction with refined ligand-binding poses through molecular docking","volume":"46","author":"Wu","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2022070500014990400_B11","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/s13321-020-00440-9","article-title":"EDock: blind protein\u2013ligand docking by replica-exchange monte carlo simulation","volume":"12","author":"Zhang","year":"2020","journal-title":"J. Cheminform."},{"key":"2022070500014990400_B12","doi-asserted-by":"crossref","first-page":"W448","DOI":"10.1093\/nar\/gkv306","article-title":"MTiOpenScreen: a web server for structure-based virtual screening","volume":"43","author":"Labb\u00e9","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2022070500014990400_B13","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1038\/s41401-019-0228-6","article-title":"CB-Dock: a web server for cavity detection-guided protein\u2013ligand blind docking","volume":"41","author":"Liu","year":"2020","journal-title":"Acta Pharmacol. Sin."},{"key":"2022070500014990400_B14","doi-asserted-by":"crossref","first-page":"1674","DOI":"10.1093\/bioinformatics\/btu104","article-title":"Improved protein\u2013ligand binding affinity prediction by using a curvature-dependent surface-area model","volume":"30","author":"Cao","year":"2014","journal-title":"Bioinformatics"},{"key":"2022070500014990400_B15","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1002\/jcc.21334","article-title":"AutoDock VINA: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading","volume":"31","author":"Trott","year":"2010","journal-title":"J. Comput. Chem."},{"key":"2022070500014990400_B16","doi-asserted-by":"crossref","first-page":"3891","DOI":"10.1021\/acs.jcim.1c00203","article-title":"AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings","volume":"61","author":"Eberhardt","year":"2021","journal-title":"J. Chem. Inf. Model."},{"key":"2022070500014990400_B17","doi-asserted-by":"crossref","first-page":"101383","DOI":"10.1016\/j.jbc.2021.101383","article-title":"The Escherichia coli two-component signal sensor BarA binds protonated acetate via a conserved hydrophobic-binding pocket","volume":"297","author":"Alvarez","year":"2021","journal-title":"J. Biol. Chem."},{"key":"2022070500014990400_B18","doi-asserted-by":"crossref","first-page":"809782","DOI":"10.3389\/fmicb.2021.809782","article-title":"Curcumin inhibits membrane-damaging pore-forming function of the \u03b2-Barrel pore-forming toxin vibrio cholerae cytolysin","volume":"12","author":"Singh","year":"2022","journal-title":"Front. Microbiol."},{"key":"2022070500014990400_B19","doi-asserted-by":"crossref","first-page":"8395","DOI":"10.1021\/acs.jpcb.1c03294","article-title":"Structural decoding of a small molecular inhibitor on the binding of SARS-CoV-2 to the ACE 2 receptor","volume":"125","author":"Mishra","year":"2021","journal-title":"J. Phys. Chem. B"},{"key":"2022070500014990400_B20","doi-asserted-by":"crossref","first-page":"1279","DOI":"10.1080\/03639045.2021.1989453","article-title":"Study on the mechanism of treating COVID-19 with SHENQI wan based on network pharmacology","volume":"47","author":"Ye","year":"2021","journal-title":"Drug Dev. Ind. Pharm."},{"key":"2022070500014990400_B21","doi-asserted-by":"crossref","first-page":"2872","DOI":"10.1002\/1873-3468.14229","article-title":"SARS-CoV-2 nucleocapsid protein interacts with immunoregulators and stress granules and phase separates to form liquid droplets","volume":"595","author":"Somasekharan","year":"2021","journal-title":"FEBS Lett."},{"key":"2022070500014990400_B22","doi-asserted-by":"crossref","first-page":"173836","DOI":"10.1016\/j.ejphar.2020.173836","article-title":"Unraveling the mechanism of arbidol binding and inhibition of SARS-CoV-2: insights from atomistic simulations","volume":"894","author":"Padhi","year":"2021","journal-title":"Eur. J. Pharmacol."},{"key":"2022070500014990400_B23","first-page":"1","article-title":"Computational molecular docking and virtual screening revealed promising SARS-CoV-2 drugs. Precis","volume":"4","author":"Hosseini","year":"2021","journal-title":"Clin. Med."},{"key":"2022070500014990400_B24","doi-asserted-by":"crossref","first-page":"104063","DOI":"10.1016\/j.compbiomed.2020.104063","article-title":"In silico identification of tretinoin as a SARS-CoV-2 envelope (E) protein ion channel inhibitor","volume":"127","author":"Dey","year":"2020","journal-title":"Comput. Biol. Med."},{"key":"2022070500014990400_B25","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/1758-2946-5-24","article-title":"JSME: a free molecule editor in JavaScript","volume":"5","author":"Bienfait","year":"2013","journal-title":"J. Cheminform."},{"key":"2022070500014990400_B26","doi-asserted-by":"crossref","first-page":"W522","DOI":"10.1093\/nar\/gkm276","article-title":"PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations","volume":"35","author":"Dolinsky","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2022070500014990400_B27","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1093\/bioinformatics\/btr009","article-title":"Improved side-chain modeling by coupling clash-detection guided iterative search with rotamer relaxation","volume":"27","author":"Cao","year":"2011","journal-title":"Bioinformatics"},{"key":"2022070500014990400_B28","first-page":"810","article-title":"DRSP: a structural database for single residue substitutions in PDB","volume":"43","author":"Liu","year":"2016","journal-title":"Prog. Biochem. Biophys."},{"key":"2022070500014990400_B29","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbac087","article-title":"FitDock: protein\u2013ligand docking by template fitting","author":"Yang","year":"2022","journal-title":"Brief. Bioinform."},{"key":"2022070500014990400_B30","doi-asserted-by":"crossref","first-page":"W576","DOI":"10.1093\/nar\/gkv402","article-title":"NGL viewer: a web application for molecular visualization","volume":"43","author":"Rose","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2022070500014990400_B31","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2022070500014990400_B32","doi-asserted-by":"crossref","first-page":"e2112621118","DOI":"10.1073\/pnas.2112621118","article-title":"Leveraging nonstructural data to predict structures and affinities of protein\u2013ligand complexes","volume":"118","author":"Paggi","year":"2021","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2022070500014990400_B33","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1186\/s13321-020-00440-9","article-title":"EDock: blind protein\u2013ligand docking by replica-exchange monte carlo simulation","volume":"12","author":"Zhang","year":"2020","journal-title":"J. Cheminform."},{"key":"2022070500014990400_B34","doi-asserted-by":"crossref","first-page":"D1096","DOI":"10.1093\/nar\/gks966","article-title":"BioLiP: a semi-manually curated database for biologically relevant ligand\u2013protein interactions","volume":"41","author":"Yang","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2022070500014990400_B35","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1758-2946-3-33","article-title":"Open babel: an open chemical toolbox","volume":"3","author":"O\u2019Boyle","year":"2011","journal-title":"J. Cheminform."},{"issue":"Suppl. 2","key":"2022070500014990400_B36","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1002\/prot.24495","article-title":"Assessment of ligand binding site predictions in CASP10","volume":"82","author":"Gallo\u00a0Cassarino","year":"2014","journal-title":"Proteins"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/W1\/W159\/44379780\/gkac394.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/W1\/W159\/44379780\/gkac394.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,21]],"date-time":"2023-11-21T03:17:24Z","timestamp":1700536644000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/W1\/W159\/6591526"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,5,24]]},"references-count":36,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2022,5,24]]},"published-print":{"date-parts":[[2022,7,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkac394","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,7,5]]},"published":{"date-parts":[[2022,5,24]]}}}