{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T18:34:49Z","timestamp":1784399689149,"version":"3.55.0"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2025,3,10]],"date-time":"2025-03-10T00:00:00Z","timestamp":1741564800000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang"},{"name":"Chinese Academy of Medical Sciences & Peking Union Medical College, Union Medical College Young Scholar Support Program, Fundamental Research Funds for the Provincial Universities of Zhejiang"},{"name":"Postdoctoral Fellowship Program of CPSF"},{"name":"Youth Project of Zhejiang Provincial Natural Science Foundation of China"},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Protein\u2013ligand docking plays a pivotal role in virtual drug screening, and recent advancements in cryo-electron microscopy (cryo-EM) technology have significantly accelerated the progress of structure-based drug discovery. However, the majority of cryo-EM density maps are of medium to low resolution (3\u201310\u00a0\u00c5), which presents challenges in effectively integrating cryo-EM data into molecular docking workflows. In this study, we present an updated protein\u2013ligand docking method, DockEM, which leverages local cryo-EM density maps and physical energy refinement to precisely dock ligands into specific protein binding sites. Tested on a dataset of 121 protein\u2013ligand compound, our results demonstrate that DockEM outperforms other advanced docking methods. The strength of DockEM lies in its ability to incorporate cryo-EM density map information, effectively leveraging the structural information of ligands embedded within these maps. This advancement enhances the use of cryo-EM density maps in virtual drug screening, offering a more reliable framework for drug discovery.<\/jats:p>","DOI":"10.1093\/bib\/bbaf091","type":"journal-article","created":{"date-parts":[[2025,3,10]],"date-time":"2025-03-10T10:54:57Z","timestamp":1741604097000},"source":"Crossref","is-referenced-by-count":4,"title":["DockEM: an enhanced method for atomic-scale protein\u2013ligand docking refinement leveraging low-to-medium resolution cryo-EM density maps"],"prefix":"10.1093","volume":"26","author":[{"given":"Jing","family":"Zou","sequence":"first","affiliation":[{"name":"College of Information Engineering, Zhejiang University of Technology , 288 Liuhe Road, Liuxia Street, Xihu District, Hangzhou 310023 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenyi","family":"Zhang","sequence":"additional","affiliation":[{"name":"Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine , 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