{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T16:12:47Z","timestamp":1772208767568,"version":"3.50.1"},"reference-count":64,"publisher":"American Chemical Society (ACS)","issue":"14","license":[{"start":{"date-parts":[[2024,7,2]],"date-time":"2024-07-02T00:00:00Z","timestamp":1719878400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2024,7,2]],"date-time":"2024-07-02T00:00:00Z","timestamp":1719878400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2024,7,2]],"date-time":"2024-07-02T00:00:00Z","timestamp":1719878400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2024,7,22]]},"DOI":"10.1021\/acs.jcim.4c00343","type":"journal-article","created":{"date-parts":[[2024,7,2]],"date-time":"2024-07-02T05:39:18Z","timestamp":1719898758000},"page":"5357-5364","source":"Crossref","is-referenced-by-count":22,"title":["Automated Absolute Binding Free Energy Calculation Workflow for Drug Discovery"],"prefix":"10.1021","volume":"64","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0945-8304","authenticated-orcid":true,"given":"Benjamin","family":"Ries","sequence":"first","affiliation":[{"name":"Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str 65, 88397 Biberach an der Riss, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5787-9130","authenticated-orcid":true,"given":"Irfan","family":"Alibay","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, The University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nithishwer Mouroug","family":"Anand","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, The University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5100-8836","authenticated-orcid":true,"given":"Philip C.","family":"Biggin","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, The University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3385-964X","authenticated-orcid":true,"given":"Aniket","family":"Magarkar","sequence":"additional","affiliation":[{"name":"Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str 65, 88397 Biberach an der Riss, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"316","published-online":{"date-parts":[[2024,7,2]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.1021\/bk-2021-1397.ch001"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1017\/S0033583511000096"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1021\/ct5000296"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.1021\/ja512751q"},{"key":"ref5\/cit5","doi-asserted-by":"crossref","unstructured":"Mobley, D. L.; Gilson, M. K. Predicting Binding Free Energies: Frontiers and Benchmarks.  bioRxiv Preprint, 2016.","DOI":"10.1101\/074625"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.7b01298"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2011.01.011"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-010-9363-3"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1186\/s13321-019-0348-5"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1038\/s42004-023-00859-9"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevMaterials.5.103801"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.23804"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.5b00368"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.1c00215"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-013-9678-y"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.1c00428"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.21105\/joss.01831"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","unstructured":"Gowers, R. J.; Alibay, I.; Swenson, D. W.; Henry, M. M.; Ries, B.; Baumann, H. M.; Eastwood, J. R. B. The Open Free Energy library, 2023. 10.5281\/zenodo.8344248.","DOI":"10.5281\/zenodo.8344248"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.6b00991"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-021-00436-z"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1021\/ci5004027"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1021\/jp0217839"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1039\/C5SC02678D"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.8b01472"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.2c00796"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2009.09.049"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2007.06.002"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.6b01183"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1063\/1.1999637"},{"key":"ref30\/cit30","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.106.084301"},{"key":"ref31\/cit31","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.1c00269"},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-80769-1"},{"key":"ref33\/cit33","doi-asserted-by":"crossref","unstructured":"Heinzelmann, G.; Huggins, D.; Gilson, M. BAT2: An Open-Source Tool for Flexible, automated and Low Cost Absolute Binding Free Energy Calculations.  ChemRxiv Preprint, 2024.","DOI":"10.26434\/chemrxiv-2024-nzt5j"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.1c00747"},{"key":"ref35\/cit35","doi-asserted-by":"publisher","DOI":"10.1007\/s10822-013-9689-8"},{"key":"ref36\/cit36","doi-asserted-by":"crossref","unstructured":"Meier, K.; Bluck, J. P.; Christ, C. D. Free Energy Methods in Drug Discovery: Current State and Future Directions; American Chemical Society, 2021; Volume 1397, Chapter 2, pp 39\u201366.","DOI":"10.1021\/bk-2021-1397.ch002"},{"key":"ref37\/cit37","doi-asserted-by":"publisher","DOI":"10.1038\/s42004-022-00721-4"},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-3495(97)78756-3"},{"key":"ref39\/cit39","volume-title":"Python 3 Reference Manual","author":"Van Rossum G.","year":"2009"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.12688\/f1000research.29032.2"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.1002\/prot.22711"},{"key":"ref42\/cit42","doi-asserted-by":"crossref","unstructured":"Boothroyd, S.; Behara, P. K.; Madin, O.; Hahn, D.; Jang, H.; Vytautas, G.; Wagner, J.; Horton, J.; Dotson, D.; Thompson, M.; Maat, J.; Wang, L.P.; Gokey, T.; Cole, D.; Gilson, M.; Chodera, J.; Bayly, C.; Shirts, M.; Mobley, D. Development and Benchmarking of Open Force Field 2.0.0 \u2500 the Sage Small Molecule Force Field.  ChemRxiv Preprint, 2022.","DOI":"10.26434\/chemrxiv-2022-n2z1c"},{"key":"ref43\/cit43","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20035"},{"key":"ref44\/cit44","doi-asserted-by":"publisher","DOI":"10.1021\/ct5010406"},{"key":"ref45\/cit45","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(199906)20:8<786::AID-JCC5>3.0.CO;2-B"},{"key":"ref46\/cit46","doi-asserted-by":"publisher","DOI":"10.1063\/1.445869"},{"key":"ref47\/cit47","doi-asserted-by":"publisher","DOI":"10.1021\/ja00392a016"},{"key":"ref48\/cit48","doi-asserted-by":"publisher","DOI":"10.1021\/ct700200b"},{"key":"ref49\/cit49","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H"},{"key":"ref50\/cit50","doi-asserted-by":"publisher","DOI":"10.1080\/08927028808080941"},{"key":"ref51\/cit51","doi-asserted-by":"publisher","DOI":"10.1021\/ct3000876"},{"key":"ref52\/cit52","doi-asserted-by":"publisher","DOI":"10.1063\/1.448118"},{"key":"ref53\/cit53","doi-asserted-by":"publisher","DOI":"10.1063\/1.328693"},{"key":"ref54\/cit54","doi-asserted-by":"publisher","unstructured":"Alibay, I. IAlibay\/MDRestraintsGenerator: v0.2.1, 2022. 10.5281\/zenodo.6977294.","DOI":"10.5281\/zenodo.6977294"},{"key":"ref55\/cit55","doi-asserted-by":"publisher","DOI":"10.1063\/1.1749657"},{"key":"ref56\/cit56","doi-asserted-by":"publisher","unstructured":"Beckstein, O.; Dotson, D. L.; Wu, Z.; Wille, D.; Marson, D.; Kenney, I.; shuail; Lee, H.; trje3733; Lim, V.; Schlaich, A.; Alibay, I.; H\u00e9nin, J.; Barhaghi, M. S.; Merz, P.; Joseph, T.; Hsu, W.T. hl2500 alchemistry\/alchemlyb: 2.2.0.  Zendo, 2024; 10.5281\/zenodo.10936440.","DOI":"10.5281\/zenodo.10936440"},{"key":"ref57\/cit57","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.0c00077"},{"key":"ref58\/cit58","doi-asserted-by":"publisher","DOI":"10.1063\/1.2978177"},{"key":"ref59\/cit59","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.20291"},{"key":"ref60\/cit60","volume-title":"GROMACS 2021 Manual","author":"Lindahl E.","year":"2021"},{"key":"ref61\/cit61","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.235"},{"key":"ref62\/cit62","doi-asserted-by":"publisher","unstructured":"The conda-forge\nProject: Community-Based Software Distribution Built on the conda\nPackage Format and Ecosystem; Zendo, 2015. 10.5281\/zenodo.4774216.","DOI":"10.5281\/zenodo.4774216"},{"key":"ref63\/cit63","doi-asserted-by":"publisher","DOI":"10.1016\/j.bmcl.2019.126717"},{"key":"ref64\/cit64","doi-asserted-by":"publisher","DOI":"10.1021\/jm100059d"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.4c00343","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.4c00343","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,22]],"date-time":"2024-07-22T08:38:09Z","timestamp":1721637489000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.4c00343"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,7,2]]},"references-count":64,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2024,7,22]]}},"alternative-id":["10.1021\/acs.jcim.4c00343"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.4c00343","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,7,2]]}}}