{"id":"https://openalex.org/W4376129086","doi":"https://doi.org/10.1021/acs.jcim.3c00013","title":"Enhancing Hit Discovery in Virtual Screening through Absolute Protein\u2013Ligand Binding Free-Energy Calculations","display_name":"Enhancing Hit Discovery in Virtual Screening through Absolute Protein\u2013Ligand Binding Free-Energy Calculations","publication_year":2023,"publication_date":"2023-05-11","ids":{"openalex":"https://openalex.org/W4376129086","doi":"https://doi.org/10.1021/acs.jcim.3c00013","pmid":"https://pubmed.ncbi.nlm.nih.gov/37167486"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c00013","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00013","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/A5100344429","display_name":"Wei Chen","orcid":"https://orcid.org/0000-0002-4015-6021"},"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":"Wei Chen","raw_affiliation_strings":["Schr\u00f6dinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070866400","display_name":"Di Cui","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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Di Cui","raw_affiliation_strings":["Schr\u00f6dinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088331520","display_name":"Steven V. Jerome","orcid":"https://orcid.org/0000-0001-7510-9682"},"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":"Steven V. Jerome","raw_affiliation_strings":["Schr\u00f6dinger, Inc., 10201 Wateridge Circle, Suite 220, San Diego, California 92121, United States"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, Inc., 10201 Wateridge Circle, Suite 220, San Diego, California 92121, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079371113","display_name":"Mayako Michino","orcid":"https://orcid.org/0000-0002-5469-025X"},"institutions":[{"id":"https://openalex.org/I4210153054","display_name":"Tri-Institutional Therapeutics Discovery Institute","ror":"https://ror.org/053z9p797","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210153054"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mayako Michino","raw_affiliation_strings":["Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th Street, New York, New York 10065, United States"],"affiliations":[{"raw_affiliation_string":"Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th Street, New York, New York 10065, United States","institution_ids":["https://openalex.org/I4210153054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059420065","display_name":"Eelke B. Lenselink","orcid":"https://orcid.org/0000-0001-5459-2978"},"institutions":[{"id":"https://openalex.org/I85459889","display_name":"Galapagos (Belgium)","ror":"https://ror.org/04e4j5d46","country_code":"BE","type":"company","lineage":["https://openalex.org/I85459889"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Eelke B. Lenselink","raw_affiliation_strings":["Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium"],"affiliations":[{"raw_affiliation_string":"Galapagos NV, Generaal De Wittelaan L11 A3, 2800 Mechelen, Belgium","institution_ids":["https://openalex.org/I85459889"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000950100","display_name":"David J. Huggins","orcid":"https://orcid.org/0000-0003-1579-2496"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I4210153054","display_name":"Tri-Institutional Therapeutics Discovery Institute","ror":"https://ror.org/053z9p797","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210153054"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David J. Huggins","raw_affiliation_strings":["Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States","Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th Street, New York, New York 10065, United States"],"affiliations":[{"raw_affiliation_string":"Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, New York 10065, United States","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Tri-Institutional Therapeutics Discovery Institute, 413 E. 69th Street, New York, New York 10065, United States","institution_ids":["https://openalex.org/I4210153054"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081868256","display_name":"Alexandre Beautrait","orcid":"https://orcid.org/0000-0001-8418-799X"},"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":"Alexandre Beautrait","raw_affiliation_strings":["Schr\u00f6dinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028940929","display_name":"J\u00e9r\u00e9mie Vend\u00f4me","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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremie Vendome","raw_affiliation_strings":["Schr\u00f6dinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017942901","display_name":"Robert Abel","orcid":"https://orcid.org/0000-0003-2945-3145"},"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":"Robert Abel","raw_affiliation_strings":["Schr\u00f6dinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012437524","display_name":"Richard A. Friesner","orcid":"https://orcid.org/0000-0002-1708-9342"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard A. Friesner","raw_affiliation_strings":["Department of Chemistry, Columbia University, New York, New York 10027, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry, Columbia University, New York, New York 10027, United States","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"last","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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lingle Wang","raw_affiliation_strings":["Schr\u00f6dinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States"],"affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger, Inc., 1540 Broadway, 24th Floor, New York, New York 10036, United States","institution_ids":["https://openalex.org/I203455613"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5059420065","https://openalex.org/A5073422740","https://openalex.org/A5079371113"],"corresponding_institution_ids":["https://openalex.org/I203455613","https://openalex.org/I4210153054","https://openalex.org/I85459889"],"apc_list":null,"apc_paid":null,"fwci":22.9787,"has_fulltext":false,"cited_by_count":116,"citation_normalized_percentile":{"value":0.99666811,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"63","issue":"10","first_page":"3171","last_page":"3185"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9998000264167786,"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9987000226974487,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.6955499053001404},{"id":"https://openalex.org/keywords/free-energy-perturbation","display_name":"Free energy perturbation","score":0.6599529981613159},{"id":"https://openalex.org/keywords/metadynamics","display_name":"Metadynamics","score":0.6441398859024048},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.58615642786026},{"id":"https://openalex.org/keywords/docking","display_name":"Docking (animal)","score":0.4846785366535187},{"id":"https://openalex.org/keywords/protein-ligand","display_name":"Protein ligand","score":0.47844862937927246},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.46011123061180115},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4499160945415497},{"id":"https://openalex.org/keywords/mean-squared-error","display_name":"Mean squared error","score":0.41685575246810913},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.40256941318511963},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.3139437437057495},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13676917552947998},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.11337083578109741},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10201594233512878},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.09698262810707092}],"concepts":[{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.6955499053001404},{"id":"https://openalex.org/C162641036","wikidata":"https://www.wikidata.org/wiki/Q5500215","display_name":"Free energy perturbation","level":3,"score":0.6599529981613159},{"id":"https://openalex.org/C62752575","wikidata":"https://www.wikidata.org/wiki/Q6822487","display_name":"Metadynamics","level":3,"score":0.6441398859024048},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.58615642786026},{"id":"https://openalex.org/C41685203","wikidata":"https://www.wikidata.org/wiki/Q1974042","display_name":"Docking (animal)","level":2,"score":0.4846785366535187},{"id":"https://openalex.org/C109095088","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Protein ligand","level":2,"score":0.47844862937927246},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.46011123061180115},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4499160945415497},{"id":"https://openalex.org/C139945424","wikidata":"https://www.wikidata.org/wiki/Q1940696","display_name":"Mean squared error","level":2,"score":0.41685575246810913},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.40256941318511963},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.3139437437057495},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13676917552947998},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.11337083578109741},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10201594233512878},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.09698262810707092},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.0},{"id":"https://openalex.org/C159110408","wikidata":"https://www.wikidata.org/wiki/Q121176","display_name":"Nursing","level":1,"score":0.0}],"mesh":[{"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","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":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.3c00013","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c00013","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:37167486","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37167486","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":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.8500000238418579}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309468","display_name":"Memorial Sloan-Kettering Cancer Center","ror":"https://ror.org/02yrq0923"},{"id":"https://openalex.org/F4320310465","display_name":"Takeda Pharmaceutical Company","ror":"https://ror.org/04hjbmv12"},{"id":"https://openalex.org/F4320313189","display_name":"Rockefeller University","ror":"https://ror.org/0420db125"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":74,"referenced_works":["https://openalex.org/W1491824558","https://openalex.org/W1971652848","https://openalex.org/W1978393297","https://openalex.org/W1980989103","https://openalex.org/W1984052581","https://openalex.org/W1984481443","https://openalex.org/W1985588649","https://openalex.org/W1987275960","https://openalex.org/W2001368885","https://openalex.org/W2017829285","https://openalex.org/W2020265146","https://openalex.org/W2024553805","https://openalex.org/W2025006523","https://openalex.org/W2031168104","https://openalex.org/W2037652551","https://openalex.org/W2037652830","https://openalex.org/W2042980919","https://openalex.org/W2048524630","https://openalex.org/W2050273205","https://openalex.org/W2052578867","https://openalex.org/W2056728743","https://openalex.org/W2062792224","https://openalex.org/W2067371805","https://openalex.org/W2072604508","https://openalex.org/W2073714240","https://openalex.org/W2088542750","https://openalex.org/W2091286894","https://openalex.org/W2091562724","https://openalex.org/W2103034037","https://openalex.org/W2112411768","https://openalex.org/W2118571345","https://openalex.org/W2120408260","https://openalex.org/W2120987099","https://openalex.org/W2128494768","https://openalex.org/W2130479394","https://openalex.org/W2132776121","https://openalex.org/W2136805944","https://openalex.org/W2140151763","https://openalex.org/W2140247386","https://openalex.org/W2154670681","https://openalex.org/W2323252543","https://openalex.org/W2323942455","https://openalex.org/W2333340978","https://openalex.org/W2524135337","https://openalex.org/W2552522590","https://openalex.org/W2560705618","https://openalex.org/W2560915683","https://openalex.org/W2618361354","https://openalex.org/W2621922190","https://openalex.org/W2730519791","https://openalex.org/W2768019189","https://openalex.org/W2772606519","https://openalex.org/W2896002068","https://openalex.org/W2899481329","https://openalex.org/W2914266147","https://openalex.org/W2952635193","https://openalex.org/W2983474927","https://openalex.org/W2990010612","https://openalex.org/W3022846064","https://openalex.org/W3027827456","https://openalex.org/W3034934060","https://openalex.org/W3054319032","https://openalex.org/W3087004338","https://openalex.org/W3087352249","https://openalex.org/W3114459216","https://openalex.org/W3118488899","https://openalex.org/W3125197509","https://openalex.org/W3135642867","https://openalex.org/W3163631242","https://openalex.org/W3167019654","https://openalex.org/W3203204467","https://openalex.org/W4220686399","https://openalex.org/W4291020694","https://openalex.org/W4297241653"],"related_works":["https://openalex.org/W3022846064","https://openalex.org/W4380716331","https://openalex.org/W2773493604","https://openalex.org/W2269591907","https://openalex.org/W2027065525","https://openalex.org/W2057846043","https://openalex.org/W2093426296","https://openalex.org/W2336040088","https://openalex.org/W2038399774","https://openalex.org/W2750247885"],"abstract_inverted_index":{"In":[0,55],"the":[1,49,73,97,129,145,148,153,169,177,183,189,196,206,210,228,262],"hit":[2,50,223,229,263,270],"identification":[3],"stage":[4],"of":[5,39,62,124,140,147,198,209,244],"drug":[6],"discovery,":[7],"a":[8,32,121,257],"diverse":[9],"chemical":[10],"space":[11],"needs":[12],"to":[13,16,21,82,103,151,188,233,260],"be":[14],"explored":[15],"identify":[17],"initial":[18],"hits.":[19],"Contrary":[20],"empirical":[22],"scoring":[23],"functions,":[24],"absolute":[25],"protein-ligand":[26,40],"binding":[27,41,81,113,202],"free-energy":[28],"perturbation":[29],"(ABFEP)":[30],"provides":[31],"theoretically":[33],"more":[34],"rigorous":[35],"and":[36,43,65,89,172,179],"accurate":[37,64],"description":[38],"thermodynamics":[42],"could,":[44],"in":[45,52,69,106,217,246,251,265],"principle,":[46],"greatly":[47,226],"improve":[48,261],"rates":[51,230,264],"virtual":[53,219,266],"screening.":[54],"this":[56,252],"work,":[57],"we":[58,166,213],"describe":[59],"an":[60,63,135],"implementation":[61],"reliable":[66],"ABFEP":[67,74,158,200,215,225,245],"method":[68,75],"FEP+.":[70],"We":[71,132],"validated":[72],"on":[76],"eight":[77,83],"congeneric":[78],"compound":[79],"series":[80],"protein":[84,164,170,190],"receptors":[85],"including":[86],"both":[87],"neutral":[88],"charged":[90],"ligands.":[91],"For":[92],"ligands":[93],"with":[94,117,120],"net":[95],"charges,":[96],"alchemical":[98],"ion":[99],"approach":[100],"is":[101],"adopted":[102],"avoid":[104],"artifacts":[105],"electrostatic":[107],"potential":[108],"energy":[109,193],"calculations.":[110],"The":[111,241],"calculated":[112,201],"free":[114,192,203],"energies":[115,204],"correlate":[116],"experimental":[118,155],"results":[119],"weighted":[122],"average":[123,154],"<i>R</i><sup>2</sup>":[125],"=":[126],"0.55":[127],"for":[128,222],"entire":[130],"dataset.":[131],"also":[133],"observe":[134],"overall":[136],"root-mean-square":[137],"error":[138],"(RMSE)":[139],"1.1":[141],"kcal/mol":[142],"after":[143],"shifting":[144],"zero-point":[146],"simulation":[149],"data":[150],"match":[152],"values.":[156],"Through":[157],"calculations":[159,216],"using":[160,205],"apo":[161,178],"versus":[162],"holo":[163,180,207],"structures,":[165],"demonstrated":[167,250],"that":[168],"conformational":[171],"protonation":[173],"state":[174],"changes":[175],"between":[176],"proteins":[181],"are":[182],"main":[184],"physical":[185],"factors":[186],"contributing":[187],"reorganization":[191],"manifested":[194],"by":[195],"overestimation":[197],"raw":[199],"structures":[208],"proteins.":[211],"Furthermore,":[212],"performed":[214],"three":[218],"screening":[220],"applications":[221],"enrichment.":[224],"improves":[227],"as":[231,256],"compared":[232],"docking":[234],"scores":[235],"or":[236],"other":[237],"methods":[238],"like":[239],"metadynamics.":[240],"good":[242],"performance":[243],"rank":[247],"ordering":[248],"compounds":[249],"work":[253],"confirms":[254],"it":[255],"useful":[258],"tool":[259],"screening,":[267],"thus":[268],"facilitating":[269],"discovery.":[271]},"counts_by_year":[{"year":2026,"cited_by_count":12},{"year":2025,"cited_by_count":35},{"year":2024,"cited_by_count":43},{"year":2023,"cited_by_count":26}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
