{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,26]],"date-time":"2026-03-26T17:32:46Z","timestamp":1774546366272,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2021,9,21]],"date-time":"2021-09-21T00:00:00Z","timestamp":1632182400000},"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":["61902352"],"award-info":[{"award-number":["61902352"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62072243"],"award-info":[{"award-number":["62072243"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61772273"],"award-info":[{"award-number":["61772273"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61773346"],"award-info":[{"award-number":["61773346"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004731","name":"Natural Science Foundation of Zhejiang","doi-asserted-by":"crossref","award":["LY21F020025"],"award-info":[{"award-number":["LY21F020025"]}],"id":[{"id":"10.13039\/501100004731","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004731","name":"Natural Science Foundation of Zhejiang","doi-asserted-by":"crossref","award":["LZ20F030002"],"award-info":[{"award-number":["LZ20F030002"]}],"id":[{"id":"10.13039\/501100004731","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Fundamental Research Funds for the Provincial Universities of Zhejiang","award":["RF-A20200012"],"award-info":[{"award-number":["RF-A20200012"]}]},{"name":"Natural Science Foundation of Jiangsu","award":["BK20201304"],"award-info":[{"award-number":["BK20201304"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,3]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Accurately identifying protein\u2013ATP binding poses is significantly valuable for both basic structure biology and drug discovery. Although many docking methods have been designed, most of them require a user-defined binding site and are difficult to achieve a high-quality protein\u2013ATP docking result. It is critical to develop a protein\u2013ATP-specific blind docking method without user-defined binding sites.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here, we present ATPdock, a template-based method for docking ATP into protein. For each query protein, if no pocket site is given, ATPdock first identifies its most potential pocket using ATPbind, an ATP-binding site predictor; then, the template pocket, which is most similar to the given or identified pocket, is searched from the database of pocket\u2013ligand structures using APoc, a pocket structural alignment tool; thirdly, the rough docking pose of ATP (rdATP) is generated using LS-align, a ligand structural alignment tool, to align the initial ATP pose to the template ligand corresponding to template pocket; finally, the Metropolis Monte Carlo simulation is used to fine-tune the rdATP under the guidance of AutoDock Vina energy function. Benchmark tests show that ATPdock significantly outperforms other state-of-the-art methods in docking accuracy.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>https:\/\/jun-csbio.github.io\/atpdock\/.<\/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\/btab667","type":"journal-article","created":{"date-parts":[[2021,9,18]],"date-time":"2021-09-18T11:09:17Z","timestamp":1631963357000},"page":"556-558","source":"Crossref","is-referenced-by-count":9,"title":["ATPdock: a template-based method for ATP-specific protein\u2013ligand docking"],"prefix":"10.1093","volume":"38","author":[{"given":"Liang","family":"Rao","sequence":"first","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ning-Xin","family":"Jia","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9202-7515","authenticated-orcid":false,"given":"Jun","family":"Hu","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6786-8053","authenticated-orcid":false,"given":"Dong-Jun","family":"Yu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Nanjing University of Science and Technology , Nanjing 210094, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7815-5884","authenticated-orcid":false,"given":"Gui-Jun","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , Hangzhou 310023, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,9,21]]},"reference":[{"key":"2023020108442732100_btab667-B1","doi-asserted-by":"crossref","first-page":"1132","DOI":"10.1002\/jcc.23905","article-title":"DOCK 6: impact of new features and current docking performance","volume":"36","author":"Allen","year":"2015","journal-title":"J. Comput. Chem"},{"key":"2023020108442732100_btab667-B2","doi-asserted-by":"crossref","first-page":"D464","DOI":"10.1093\/nar\/gky1004","article-title":"RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy","volume":"47","author":"Burley","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023020108442732100_btab667-B3","doi-asserted-by":"crossref","first-page":"2648","DOI":"10.1073\/pnas.1522966113","article-title":"ATP binding by the P-loop NTPase OsYchF1 (an unconventional G protein) contributes to biotic but not abiotic stress responses","volume":"113","author":"Cheung","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023020108442732100_btab667-B4","doi-asserted-by":"crossref","first-page":"6502","DOI":"10.1021\/acs.jcim.0c01095","article-title":"A consistent scheme for gradient-based optimization of protein\u2013ligand poses","volume":"60","author":"Flachsenberg","year":"2020","journal-title":"J. Chem. Inf. Model"},{"key":"2023020108442732100_btab667-B5","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1093\/bioinformatics\/btt024","article-title":"APoc: large scale identification of similar protein pockets","volume":"29","author":"Gao","year":"2013","journal-title":"Bioinformatics"},{"key":"2023020108442732100_btab667-B6","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1021\/acs.jcim.7b00397","article-title":"ATPbind: accurate protein\u2013ATP binding site prediction by combining sequence-profiling and structure-based comparisons","volume":"58","author":"Hu","year":"2018","journal-title":"J. Chem. Inf. 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