{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T12:58:26Z","timestamp":1776085106721,"version":"3.50.1"},"reference-count":110,"publisher":"American Chemical Society (ACS)","issue":"7","license":[{"start":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T00:00:00Z","timestamp":1773878400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100031478","name":"NextGenerationEU","doi-asserted-by":"publisher","award":["J33C22001130001 CN00000041"],"award-info":[{"award-number":["J33C22001130001 CN00000041"]}],"id":[{"id":"10.13039\/100031478","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100031478","name":"NextGenerationEU","doi-asserted-by":"publisher","award":["J33C22001180001 CN00000013"],"award-info":[{"award-number":["J33C22001180001 CN00000013"]}],"id":[{"id":"10.13039\/100031478","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Chem. Inf. Model."],"published-print":{"date-parts":[[2026,4,13]]},"DOI":"10.1021\/acs.jcim.5c02955","type":"journal-article","created":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T17:05:06Z","timestamp":1773939906000},"page":"4187-4201","source":"Crossref","is-referenced-by-count":0,"title":["Critical Assessment of a Structure-Based Pipeline for Targeting the Long Noncoding RNA MALAT1"],"prefix":"10.1021","volume":"66","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2202-2000","authenticated-orcid":true,"given":"Riccardo","family":"Aguti","sequence":"first","affiliation":[{"name":"Department of Pharmacy and Biotechnology, Alma Mater Studiorum","place":["Bologna, Italy"]},{"name":"Universit\u00e0 di Bologna","place":["Bologna, Italy"]},{"name":"Computational and Chemical Biology","place":["Genova, Italy"]},{"name":"Istituto Italiano di Tecnologia","place":["Genova, Italy"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4373-9310","authenticated-orcid":true,"given":"Mattia","family":"Bernetti","sequence":"additional","affiliation":[{"name":"Computational and Chemical Biology","place":["Genova, Italy"]},{"name":"Istituto Italiano di Tecnologia","place":["Genova, Italy"]},{"name":"Department of Biomolecular Sciences (DISB)","place":["Urbino, Italy"]},{"name":"Universit\u00e0 degli Studi di Urbino \u201cCarlo Bo\u201d","place":["Urbino, Italy"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9071-5621","authenticated-orcid":true,"given":"Gian Marco","family":"Elisi","sequence":"additional","affiliation":[{"name":"Department of Biomolecular Sciences (DISB)","place":["Urbino, Italy"]},{"name":"Universit\u00e0 degli Studi di Urbino \u201cCarlo Bo\u201d","place":["Urbino, Italy"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6370-1176","authenticated-orcid":true,"given":"Andrea","family":"Cavalli","sequence":"additional","affiliation":[{"name":"Department of Pharmacy and Biotechnology, Alma Mater Studiorum","place":["Bologna, Italy"]},{"name":"Universit\u00e0 di Bologna","place":["Bologna, Italy"]},{"name":"Computational and Chemical Biology","place":["Genova, Italy"]},{"name":"Istituto Italiano di Tecnologia","place":["Genova, Italy"]},{"name":"Centre Europ\u00e9en de Calcul Atomique et Mol\u00e9culaire (CECAM)","place":["Lausanne, Switzerland"]},{"name":"Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne","place":["Lausanne, Switzerland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3757-7802","authenticated-orcid":true,"given":"Matteo","family":"Masetti","sequence":"additional","affiliation":[{"name":"Department of Pharmacy and Biotechnology, Alma Mater Studiorum","place":["Bologna, Italy"]},{"name":"Universit\u00e0 di Bologna","place":["Bologna, Italy"]}]}],"member":"316","published-online":{"date-parts":[[2026,3,19]]},"reference":[{"key":"ref1\/cit1","doi-asserted-by":"publisher","DOI":"10.1101\/gad.1800909"},{"key":"ref2\/cit2","doi-asserted-by":"publisher","DOI":"10.1038\/nature11247"},{"key":"ref3\/cit3","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(00)80284-6"},{"key":"ref4\/cit4","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3681"},{"key":"ref5\/cit5","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2014.03.008"},{"key":"ref6\/cit6","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbrc.2012.12.074"},{"key":"ref7\/cit7","doi-asserted-by":"publisher","DOI":"10.1158\/2159-8290.CD-11-0209"},{"key":"ref8\/cit8","doi-asserted-by":"publisher","DOI":"10.1016\/j.tig.2017.08.002"},{"key":"ref9\/cit9","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biochem-051410-092902"},{"key":"ref10\/cit10","doi-asserted-by":"publisher","DOI":"10.1038\/s41556-019-0311-8"},{"key":"ref11\/cit11","doi-asserted-by":"publisher","DOI":"10.1534\/genetics.112.146704"},{"key":"ref12\/cit12","doi-asserted-by":"publisher","DOI":"10.3390\/ijms17050702"},{"key":"ref13\/cit13","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2024.102908"},{"key":"ref14\/cit14","doi-asserted-by":"publisher","DOI":"10.1038\/nature05519"},{"key":"ref15\/cit15","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2010.09.049"},{"key":"ref16\/cit16","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2013.02.016"},{"key":"ref17\/cit17","doi-asserted-by":"publisher","DOI":"10.1038\/351153a0"},{"key":"ref18\/cit18","doi-asserted-by":"publisher","DOI":"10.1038\/415810a"},{"key":"ref19\/cit19","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3606"},{"key":"ref20\/cit20","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2013.02.012"},{"key":"ref21\/cit21","doi-asserted-by":"publisher","DOI":"10.1080\/15476286.2017.1358347"},{"key":"ref22\/cit22","doi-asserted-by":"publisher","DOI":"10.1186\/s13045-018-0606-4"},{"key":"ref23\/cit23","doi-asserted-by":"publisher","DOI":"10.1158\/0008-5472.CAN-12-2850"},{"key":"ref24\/cit24","doi-asserted-by":"publisher","DOI":"10.1101\/gad.270959.115"},{"key":"ref25\/cit25","doi-asserted-by":"publisher","DOI":"10.1080\/15476286.2019.1592072"},{"key":"ref26\/cit26","doi-asserted-by":"publisher","DOI":"10.1038\/s41588-018-0252-3"},{"key":"ref27\/cit27","doi-asserted-by":"publisher","DOI":"10.1002\/ijc.31386"},{"key":"ref28\/cit28","doi-asserted-by":"publisher","DOI":"10.1038\/sj.onc.1206928"},{"key":"ref29\/cit29","doi-asserted-by":"publisher","DOI":"10.1158\/1535-7163.MCT-16-0591"},{"key":"ref30\/cit30","doi-asserted-by":"publisher","DOI":"10.3892\/ol.2018.9293"},{"key":"ref31\/cit31","doi-asserted-by":"publisher","DOI":"10.1186\/s40364-023-00467-8"},{"key":"ref32\/cit32","doi-asserted-by":"publisher","DOI":"10.2147\/CMAR.S169406"},{"key":"ref33\/cit33","doi-asserted-by":"publisher","DOI":"10.1021\/acsmedchemlett.1c00060"},{"key":"ref34\/cit34","doi-asserted-by":"publisher","DOI":"10.1021\/acschembio.8b00807"},{"key":"ref35\/cit35","doi-asserted-by":"publisher","DOI":"10.1002\/anie.201808823"},{"key":"ref36\/cit36","doi-asserted-by":"publisher","DOI":"10.1021\/acschembio.5c00061"},{"key":"ref37\/cit37","doi-asserted-by":"publisher","DOI":"10.1002\/ardp.202300134"},{"key":"ref38\/cit38","doi-asserted-by":"publisher","DOI":"10.1007\/s00044-024-03336-7"},{"key":"ref39\/cit39","doi-asserted-by":"publisher","DOI":"10.1101\/gad.204438.112"},{"key":"ref40\/cit40","doi-asserted-by":"publisher","DOI":"10.1038\/nsmb.2844"},{"key":"ref41\/cit41","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1171"},{"key":"ref42\/cit42","doi-asserted-by":"publisher","DOI":"10.1038\/nchembio.596"},{"key":"ref43\/cit43","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmb.2003.12.046"},{"key":"ref44\/cit44","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky689"},{"key":"ref45\/cit45","doi-asserted-by":"publisher","DOI":"10.1126\/science.1096361"},{"key":"ref46\/cit46","doi-asserted-by":"publisher","DOI":"10.1038\/nrd.2018.93"},{"key":"ref47\/cit47","doi-asserted-by":"publisher","DOI":"10.1017\/qrd.2022.20"},{"key":"ref48\/cit48","doi-asserted-by":"publisher","DOI":"10.1016\/j.chempr.2021.05.021"},{"key":"ref49\/cit49","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.5c00452"},{"key":"ref50\/cit50","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.5c00814"},{"key":"ref51\/cit51","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.2c00751"},{"key":"ref52\/cit52","doi-asserted-by":"publisher","DOI":"10.1039\/D3CP04366E"},{"key":"ref53\/cit53","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jpclett.4c03456"},{"key":"ref54\/cit54","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.4c00420"},{"key":"ref55\/cit55","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.3c01533"},{"key":"ref56\/cit56","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.3c00507"},{"key":"ref57\/cit57","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.4c00235"},{"key":"ref58\/cit58","doi-asserted-by":"publisher","DOI":"10.1038\/s42003-025-08809-y"},{"key":"ref59\/cit59","doi-asserted-by":"publisher","DOI":"10.1021\/acschembio.2c00124"},{"key":"ref60\/cit60","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jmedchem.5b01684"},{"key":"ref61\/cit61","doi-asserted-by":"publisher","DOI":"10.1080\/00268976.2013.824126"},{"key":"ref62\/cit62","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.4c00773"},{"key":"ref63\/cit63","doi-asserted-by":"publisher","DOI":"10.1016\/j.str.2024.07.019"},{"key":"ref64\/cit64","doi-asserted-by":"publisher","DOI":"10.1021\/acs.chemrev.7b00427"},{"key":"ref65\/cit65","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.0c01006"},{"key":"ref66\/cit66","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003571"},{"key":"ref67\/cit67","doi-asserted-by":"publisher","DOI":"10.1002\/jcc.21256"},{"key":"ref68\/cit68","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.1c00203"},{"key":"ref69\/cit69","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1008309"},{"key":"ref70\/cit70","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.4c00681"},{"key":"ref71\/cit71","doi-asserted-by":"publisher","DOI":"10.1002\/prot.21123"},{"key":"ref72\/cit72","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.106.097782"},{"key":"ref73\/cit73","doi-asserted-by":"publisher","DOI":"10.1021\/ct200162x"},{"key":"ref74\/cit74","doi-asserted-by":"publisher","DOI":"10.1021\/jz501780a"},{"key":"ref75\/cit75","doi-asserted-by":"publisher","DOI":"10.1021\/jp8001614"},{"key":"ref76\/cit76","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H"},{"key":"ref77\/cit77","doi-asserted-by":"publisher","DOI":"10.1021\/ct700200b"},{"key":"ref78\/cit78","doi-asserted-by":"publisher","DOI":"10.1063\/1.464397"},{"key":"ref79\/cit79","doi-asserted-by":"publisher","DOI":"10.1063\/1.470117"},{"key":"ref80\/cit80","doi-asserted-by":"publisher","DOI":"10.1063\/1.2408420"},{"key":"ref81\/cit81","doi-asserted-by":"publisher","DOI":"10.1063\/5.0020514"},{"key":"ref82\/cit82","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku972"},{"key":"ref83\/cit83","doi-asserted-by":"publisher","DOI":"10.1021\/acscentsci.7b00211"},{"key":"ref84\/cit84","doi-asserted-by":"publisher","DOI":"10.1063\/5.0145364"},{"key":"ref85\/cit85","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.7b00680"},{"key":"ref86\/cit86","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0059744"},{"key":"ref87\/cit87","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.5c00821"},{"key":"ref88\/cit88","first-page":"2825","volume":"12","author":"Pedregosa F.","year":"2011","journal-title":"J. Mach. Learn. Res."},{"key":"ref89\/cit89","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.9b00558"},{"key":"ref90\/cit90","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1009783"},{"key":"ref91\/cit91","doi-asserted-by":"publisher","DOI":"10.1021\/ci400534h"},{"key":"ref92\/cit92","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.3c00596"},{"key":"ref93\/cit93","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jctc.1c00302"},{"key":"ref94\/cit94","volume-title":"Schr\u00f6dinger Release 2025\u201302: MacroModel, Schr\u00f6dinger","year":"2025"},{"key":"ref95\/cit95","doi-asserted-by":"publisher","DOI":"10.1080\/00268978400101201"},{"key":"ref96\/cit96","doi-asserted-by":"publisher","DOI":"10.1103\/PhysRevA.31.1695"},{"key":"ref97\/cit97","doi-asserted-by":"publisher","DOI":"10.1063\/1.467468"},{"key":"ref98\/cit98","doi-asserted-by":"publisher","DOI":"10.1002\/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V"},{"key":"ref99\/cit99","doi-asserted-by":"publisher","DOI":"10.1063\/1.463137"},{"key":"ref100\/cit100","volume-title":"Schr\u00f6dinger Release 2025\u201302: Desmond, Schr\u00f6dinger","year":"2025"},{"key":"ref101\/cit101","doi-asserted-by":"publisher","DOI":"10.1016\/j.bpj.2018.02.038"},{"key":"ref102\/cit102","doi-asserted-by":"publisher","DOI":"10.1039\/C4CP05262E"},{"key":"ref103\/cit103","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2018.01.004"},{"key":"ref104\/cit104","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.3c00738"},{"key":"ref105\/cit105","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2024.102820"},{"key":"ref106\/cit106","doi-asserted-by":"publisher","DOI":"10.59566\/ISRNN.2024.0101001"},{"key":"ref107\/cit107","doi-asserted-by":"publisher","DOI":"10.3390\/molecules22112029"},{"key":"ref108\/cit108","doi-asserted-by":"crossref","unstructured":"Cournia, Z.; Chipot, C.; Roux, B.; York, D. M.; Sherman, W.\n                      Free Energy Methods in Drug Discovery\u2500Introduction, Free Energy Methods in Drug Discovery: Current State and Future Directions\n                      ; American Chemical Society, 2021; Vol. 1397, pp 1\u201338.","DOI":"10.1021\/bk-2021-1397.ch001"},{"key":"ref109\/cit109","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.4c01505"},{"key":"ref110\/cit110","doi-asserted-by":"publisher","DOI":"10.1021\/acs.jcim.4c01708"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.5c02955","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.5c02955","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,13]],"date-time":"2026-04-13T12:11:28Z","timestamp":1776082288000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/doi\/10.1021\/acs.jcim.5c02955"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,19]]},"references-count":110,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2026,4,13]]}},"alternative-id":["10.1021\/acs.jcim.5c02955"],"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.5c02955","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,19]]}}}