{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,28]],"date-time":"2026-06-28T13:13:56Z","timestamp":1782652436968,"version":"3.54.5"},"reference-count":58,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2023,6,16]],"date-time":"2023-06-16T00:00:00Z","timestamp":1686873600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFA1004300"],"award-info":[{"award-number":["2022YFA1004300"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Binding free energy calculation of a ligand to a protein receptor is a fundamental objective in drug discovery. Molecular mechanics\/Generalized-Born (Poisson\u2013Boltzmann) surface area (MM\/GB(PB)SA) is one of the most popular methods for binding free energy calculations. It is more accurate than most scoring functions and more computationally efficient than alchemical free energy methods. Several open-source tools for performing MM\/GB(PB)SA calculations have been developed, but they have limitations and high entry barriers to users. Here, we introduce Uni-GBSA, a user-friendly automatic workflow to perform MM\/GB(PB)SA calculations, which can perform topology preparation, structure optimization, binding free energy calculation and parameter scanning for MM\/GB(PB)SA calculations. It also offers a batch mode that evaluates thousands of molecules against one protein target in parallel for efficient application in virtual screening. The default parameters are selected after systematic testing on the PDBBind-2011 refined dataset. In our case studies, Uni-GBSA produced a satisfactory correlation with the experimental binding affinities and outperformed AutoDock Vina in molecular enrichment. Uni-GBSA is available as an open-source package at https:\/\/github.com\/dptech-corp\/Uni-GBSA. It can also be accessed for virtual screening from the Hermite web platform at https:\/\/hermite.dp.tech. A free Uni-GBSA web server of a lab version is available at https:\/\/labs.dp.tech\/projects\/uni-gbsa\/. This increases user-friendliness because the web server frees users from package installations and provides users with validated workflows for input data and parameter settings, cloud computing resources for efficient job completions, a user-friendly interface and professional support and maintenance.<\/jats:p>","DOI":"10.1093\/bib\/bbad218","type":"journal-article","created":{"date-parts":[[2023,5,24]],"date-time":"2023-05-24T18:49:33Z","timestamp":1684954173000},"source":"Crossref","is-referenced-by-count":56,"title":["Uni-GBSA: an open-source and web-based automatic workflow to perform MM\/GB(PB)SA calculations for virtual screening"],"prefix":"10.1093","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9991-7174","authenticated-orcid":false,"given":"Maohua","family":"Yang","sequence":"first","affiliation":[{"name":"DP Technology , Beijing, 100080 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4728-2968","authenticated-orcid":false,"given":"Zonghua","family":"Bo","sequence":"additional","affiliation":[{"name":"DP Technology , Beijing, 100080 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Xu","sequence":"additional","affiliation":[{"name":"DP Technology , Beijing, 100080 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Xu","sequence":"additional","affiliation":[{"name":"DP Technology , Beijing, 100080 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0235-5994","authenticated-orcid":false,"given":"Dongdong","family":"Wang","sequence":"additional","affiliation":[{"name":"DP Technology , Beijing, 100080 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2825-0576","authenticated-orcid":false,"given":"Hang","family":"Zheng","sequence":"additional","affiliation":[{"name":"DP Technology , Beijing, 100080 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,6,16]]},"reference":[{"issue":"4","key":"2023072020144773000_ref1","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1016\/j.cbpa.2011.05.021","article-title":"Free energy calculations of protein\u2013ligand interactions","volume":"15","author":"Ruiter","year":"2011","journal-title":"Curr Opin Chem Biol"},{"issue":"5","key":"2023072020144773000_ref2","doi-asserted-by":"crossref","first-page":"407","DOI":"10.2174\/138920306778559395","article-title":"Scoring functions for protein-ligand docking","volume":"7","author":"Jain","year":"2006","journal-title":"Curr Protein Pept Sci"},{"issue":"2","key":"2023072020144773000_ref3","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"},{"issue":"1","key":"2023072020144773000_ref4","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1023\/A:1016357811882","article-title":"Further development and validation of empirical scoring functions for structure-based binding affinity prediction","volume":"16","author":"Wang","year":"2002","journal-title":"J Comput Aided Mol Des"},{"issue":"7","key":"2023072020144773000_ref5","doi-asserted-by":"crossref","first-page":"1750","DOI":"10.1021\/jm030644s","article-title":"Glide: a new approach for rapid, accurate docking and scoring. 2. 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