{"id":"https://openalex.org/W4406970630","doi":"https://doi.org/10.1021/acs.jcim.4c01708","title":"Accurate Physics-Based Prediction of Binding Affinities of RNA- and DNA-Targeting Ligands","display_name":"Accurate Physics-Based Prediction of Binding Affinities of RNA- and DNA-Targeting Ligands","publication_year":2025,"publication_date":"2025-01-30","ids":{"openalex":"https://openalex.org/W4406970630","doi":"https://doi.org/10.1021/acs.jcim.4c01708","pmid":"https://pubmed.ncbi.nlm.nih.gov/39883536"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01708","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01708","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102822851","display_name":"Ara M. Abramyan","orcid":"https://orcid.org/0009-0002-1837-2593"},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]},{"id":"https://openalex.org/I4210161498","display_name":"Schrodinger (United States)","ror":null,"country_code":"US","type":null,"lineage":["https://openalex.org/I4210161498"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ara M. Abramyan","raw_affiliation_strings":["Schr\u00f6dinger Incorporated","Schr\u00f6dinger Incorporated, San Diego, California 92121, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger Incorporated","institution_ids":["https://openalex.org/I4210161498"]},{"raw_affiliation_string":"Schr\u00f6dinger Incorporated, San Diego, California 92121, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057305493","display_name":"Anna Bochicchio","orcid":"https://orcid.org/0000-0002-4169-8332"},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anna Bochicchio","raw_affiliation_strings":["Schr\u00f6dinger GmbH","Schr\u00f6dinger GmbH, Munich 80538, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger GmbH","institution_ids":["https://openalex.org/I203455613"]},{"raw_affiliation_string":"Schr\u00f6dinger GmbH, Munich 80538, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082132832","display_name":"Chuanjie Wu","orcid":"https://orcid.org/0000-0002-0494-416X"},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]},{"id":"https://openalex.org/I4210161498","display_name":"Schrodinger (United States)","ror":null,"country_code":"US","type":null,"lineage":["https://openalex.org/I4210161498"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chuanjie Wu","raw_affiliation_strings":["Schr\u00f6dinger Incorporated","Schr\u00f6dinger Incorporated, New York, New York 10036, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger Incorporated","institution_ids":["https://openalex.org/I4210161498"]},{"raw_affiliation_string":"Schr\u00f6dinger Incorporated, New York, New York 10036, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012615940","display_name":"Wolfgang Damm","orcid":null},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]},{"id":"https://openalex.org/I4210161498","display_name":"Schrodinger (United States)","ror":null,"country_code":"US","type":null,"lineage":["https://openalex.org/I4210161498"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wolfgang Damm","raw_affiliation_strings":["Schr\u00f6dinger Incorporated","Schr\u00f6dinger Incorporated, New York, New York 10036, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger Incorporated","institution_ids":["https://openalex.org/I4210161498"]},{"raw_affiliation_string":"Schr\u00f6dinger Incorporated, New York, New York 10036, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064462016","display_name":"David R. Langley","orcid":"https://orcid.org/0000-0002-0820-3190"},"institutions":[{"id":"https://openalex.org/I4210142342","display_name":"Arvinas (United States)","ror":"https://ror.org/045jkfr03","country_code":"US","type":"company","lineage":["https://openalex.org/I4210142342"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David R. Langley","raw_affiliation_strings":["Arvinas Incorporated","Arvinas Incorporated, New Haven, Connecticut 06511, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Arvinas Incorporated","institution_ids":["https://openalex.org/I4210142342"]},{"raw_affiliation_string":"Arvinas Incorporated, New Haven, Connecticut 06511, United States","institution_ids":["https://openalex.org/I4210142342"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045373536","display_name":"Devleena Shivakumar","orcid":null},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]},{"id":"https://openalex.org/I4210161498","display_name":"Schrodinger (United States)","ror":null,"country_code":"US","type":null,"lineage":["https://openalex.org/I4210161498"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Devleena Shivakumar","raw_affiliation_strings":["Schr\u00f6dinger Incorporated","Schr\u00f6dinger Incorporated, New York, New York 10036, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger Incorporated","institution_ids":["https://openalex.org/I4210161498"]},{"raw_affiliation_string":"Schr\u00f6dinger Incorporated, New York, New York 10036, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007345837","display_name":"Dmitry Lupyan","orcid":null},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]},{"id":"https://openalex.org/I4210161498","display_name":"Schrodinger (United States)","ror":null,"country_code":"US","type":null,"lineage":["https://openalex.org/I4210161498"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dmitry Lupyan","raw_affiliation_strings":["Schr\u00f6dinger Incorporated","Schr\u00f6dinger Incorporated, Cambridge, Massachusetts 02142, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger Incorporated","institution_ids":["https://openalex.org/I4210161498"]},{"raw_affiliation_string":"Schr\u00f6dinger Incorporated, Cambridge, Massachusetts 02142, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073422740","display_name":"Lingle Wang","orcid":"https://orcid.org/0000-0002-8170-6798"},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]},{"id":"https://openalex.org/I4210161498","display_name":"Schrodinger (United States)","ror":null,"country_code":"US","type":null,"lineage":["https://openalex.org/I4210161498"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lingle Wang","raw_affiliation_strings":["Schr\u00f6dinger Incorporated","Schr\u00f6dinger Incorporated, New York, New York 10036, United States"],"raw_orcid":"https://orcid.org/0000-0002-8170-6798","affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger Incorporated","institution_ids":["https://openalex.org/I4210161498"]},{"raw_affiliation_string":"Schr\u00f6dinger Incorporated, New York, New York 10036, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045848997","display_name":"Edward Harder","orcid":"https://orcid.org/0000-0001-9213-787X"},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]},{"id":"https://openalex.org/I4210161498","display_name":"Schrodinger (United States)","ror":null,"country_code":"US","type":null,"lineage":["https://openalex.org/I4210161498"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Edward Harder","raw_affiliation_strings":["Schr\u00f6dinger Incorporated","Schr\u00f6dinger Incorporated, New York, New York 10036, United States"],"raw_orcid":"https://orcid.org/0000-0001-9213-787X","affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger Incorporated","institution_ids":["https://openalex.org/I4210161498"]},{"raw_affiliation_string":"Schr\u00f6dinger Incorporated, New York, New York 10036, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080678224","display_name":"E.O. Oloo","orcid":null},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]},{"id":"https://openalex.org/I4210161498","display_name":"Schrodinger (United States)","ror":null,"country_code":"US","type":null,"lineage":["https://openalex.org/I4210161498"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Eliud O. Oloo","raw_affiliation_strings":["Schr\u00f6dinger Incorporated","Schr\u00f6dinger Incorporated, Cambridge, Massachusetts 02142, United States"],"raw_orcid":"https://orcid.org/0009-0009-9612-9880","affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger Incorporated","institution_ids":["https://openalex.org/I4210161498"]},{"raw_affiliation_string":"Schr\u00f6dinger Incorporated, Cambridge, Massachusetts 02142, United States","institution_ids":["https://openalex.org/I203455613"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5080678224"],"corresponding_institution_ids":["https://openalex.org/I203455613","https://openalex.org/I4210161498"],"apc_list":null,"apc_paid":null,"fwci":6.3504,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.96053035,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"65","issue":"3","first_page":"1392","last_page":"1403"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9793000221252441,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.8075309991836548},{"id":"https://openalex.org/keywords/binding-affinities","display_name":"Binding affinities","score":0.8042025566101074},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6720351576805115},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.5293938517570496},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5275974869728088},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3945622444152832},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3263446092605591},{"id":"https://openalex.org/keywords/nanotechnology","display_name":"Nanotechnology","score":0.32068854570388794},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.15748271346092224},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.15716224908828735},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09494540095329285}],"concepts":[{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.8075309991836548},{"id":"https://openalex.org/C3018795828","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Binding affinities","level":3,"score":0.8042025566101074},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6720351576805115},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.5293938517570496},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5275974869728088},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3945622444152832},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3263446092605591},{"id":"https://openalex.org/C171250308","wikidata":"https://www.wikidata.org/wiki/Q11468","display_name":"Nanotechnology","level":1,"score":0.32068854570388794},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.15748271346092224},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.15716224908828735},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09494540095329285},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.4c01708","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01708","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:39883536","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39883536","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4399999976158142,"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":89,"referenced_works":["https://openalex.org/W641640508","https://openalex.org/W1584476217","https://openalex.org/W1625910593","https://openalex.org/W1965335626","https://openalex.org/W1966658247","https://openalex.org/W1966834115","https://openalex.org/W1973363995","https://openalex.org/W1974892165","https://openalex.org/W1978470647","https://openalex.org/W1985588649","https://openalex.org/W1990356245","https://openalex.org/W2009423060","https://openalex.org/W2010340383","https://openalex.org/W2014316770","https://openalex.org/W2022870729","https://openalex.org/W2027109368","https://openalex.org/W2027423337","https://openalex.org/W2027749847","https://openalex.org/W2030574185","https://openalex.org/W2031168104","https://openalex.org/W2048792281","https://openalex.org/W2049475242","https://openalex.org/W2052673986","https://openalex.org/W2058276221","https://openalex.org/W2068205741","https://openalex.org/W2080911376","https://openalex.org/W2083364776","https://openalex.org/W2083992260","https://openalex.org/W2092915328","https://openalex.org/W2092956715","https://openalex.org/W2104345366","https://openalex.org/W2107067138","https://openalex.org/W2114001343","https://openalex.org/W2124125031","https://openalex.org/W2130479394","https://openalex.org/W2154670681","https://openalex.org/W2159859043","https://openalex.org/W2166810745","https://openalex.org/W2168909179","https://openalex.org/W2175696527","https://openalex.org/W2222589778","https://openalex.org/W2256427311","https://openalex.org/W2323942455","https://openalex.org/W2500362036","https://openalex.org/W2552522590","https://openalex.org/W2730519791","https://openalex.org/W2768019189","https://openalex.org/W2886911892","https://openalex.org/W2899267520","https://openalex.org/W2899481329","https://openalex.org/W2904369940","https://openalex.org/W2911615806","https://openalex.org/W2912818999","https://openalex.org/W2943749213","https://openalex.org/W2944987824","https://openalex.org/W2945072593","https://openalex.org/W2949467224","https://openalex.org/W2951718918","https://openalex.org/W2963584667","https://openalex.org/W2969628133","https://openalex.org/W2989374524","https://openalex.org/W3004371033","https://openalex.org/W3023794997","https://openalex.org/W3027827456","https://openalex.org/W3032038485","https://openalex.org/W3084513853","https://openalex.org/W3087352249","https://openalex.org/W3095910089","https://openalex.org/W3098993911","https://openalex.org/W3114459216","https://openalex.org/W3135866733","https://openalex.org/W3138217379","https://openalex.org/W3149078497","https://openalex.org/W3160838913","https://openalex.org/W3167019654","https://openalex.org/W3217015076","https://openalex.org/W4210395111","https://openalex.org/W4214725635","https://openalex.org/W4224296001","https://openalex.org/W4285331314","https://openalex.org/W4286382909","https://openalex.org/W4290672950","https://openalex.org/W4302362590","https://openalex.org/W4376129086","https://openalex.org/W4386704695","https://openalex.org/W4387639561","https://openalex.org/W4388615763","https://openalex.org/W4389108403","https://openalex.org/W4391257042"],"related_works":["https://openalex.org/W2903287478","https://openalex.org/W2031259671","https://openalex.org/W3112966125","https://openalex.org/W1990832091","https://openalex.org/W4240532245","https://openalex.org/W4406646854","https://openalex.org/W1961356786","https://openalex.org/W4392059316","https://openalex.org/W2073233024","https://openalex.org/W1966443150"],"abstract_inverted_index":{"Accurate":[0],"prediction":[1],"of":[2,5,25,36,72,83,106,109,129,132,138,167,174,190,199,217],"the":[3,23,34,73,107,119,168,175,180,200,215],"affinity":[4],"ligand":[6],"binding":[7,81,126,150],"to":[8,28,61,66,85,90,213],"nucleic":[9,37],"acids":[10],"represents":[11],"a":[12,103,136,160,185],"formidable":[13],"challenge":[14],"for":[15,78],"current":[16],"computational":[17,26],"approaches.":[18],"This":[19],"limitation":[20],"has":[21,94,210],"hindered":[22],"use":[24],"methods":[27],"develop":[29],"small-molecule":[30],"drugs":[31],"that":[32,208],"modulate":[33],"activity":[35],"acids,":[38],"including":[39],"those":[40],"associated":[41],"with":[42,135],"anticancer,":[43],"antiviral,":[44],"and":[45,53,116,155,226],"antibacterial":[46],"effects.":[47],"In":[48,98],"recent":[49],"years,":[50],"significant":[51],"scientific":[52],"technological":[54],"advances":[55],"as":[56,58,111],"well":[57],"easier":[59],"access":[60],"compute":[62],"resources":[63],"have":[64],"contributed":[65],"free-energy":[67],"perturbation":[68],"(FEP)":[69],"becoming":[70],"one":[71,196],"most":[74],"consistently":[75],"reliable":[76],"approaches":[77],"predicting":[79,124],"relative":[80,125],"affinities":[82],"ligands":[84,93,133,147],"proteins.":[86],"Nevertheless,":[87],"FEP's":[88],"applicability":[89],"nucleic-acid":[91],"targeting":[92,224],"remained":[95],"largely":[96],"undetermined.":[97],"this":[99],"work,":[100],"we":[101,183],"present":[102],"systematic":[104],"assessment":[105],"accuracy":[108,212],"FEP,":[110],"implemented":[112],"in":[113,123,220],"FEP+":[114,209],"software":[115],"facilitated":[117],"by":[118],"OPLS4":[120],"force":[121],"field,":[122],"free":[127],"energies":[128],"congeneric":[130],"series":[131,219],"interacting":[134],"variety":[137],"DNA/RNA":[139],"systems.":[140],"The":[141],"study":[142],"encompassed":[143],"more":[144,164],"than":[145,165],"100":[146],"exhibiting":[148],"diverse":[149],"modes,":[151],"some":[152],"partially":[153],"exposed":[154],"others":[156],"deeply":[157],"buried.":[158],"Using":[159],"consistent":[161],"simulation":[162],"protocol,":[163],"half":[166],"predictions":[169],"are":[170],"within":[171,195],"1":[172],"kcal/mol":[173],"experimentally":[176,201],"measured":[177,202],"values.":[178],"Across":[179],"data":[181],"set,":[182],"report":[184],"combined":[186],"average":[187],"pairwise":[188],"root-mean-square-error":[189],"<1.4":[191],"kcal/mol,":[192],"which":[193],"falls":[194],"log":[197],"unit":[198],"dissociation":[203],"constants.":[204],"These":[205],"results":[206],"suggest":[207],"sufficient":[211],"guide":[214],"optimization":[216],"lead":[218],"drug":[221],"discovery":[222],"programs":[223],"RNA":[225],"DNA.":[227]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-07T13:39:58.223016","created_date":"2025-10-10T00:00:00"}