{"id":"https://openalex.org/W4402206730","doi":"https://doi.org/10.1021/acs.jcim.4c00464","title":"Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach","display_name":"Improvements in Precision of Relative Binding Free Energy Calculations Afforded by the Alchemical Enhanced Sampling (ACES) Approach","publication_year":2024,"publication_date":"2024-09-03","ids":{"openalex":"https://openalex.org/W4402206730","doi":"https://doi.org/10.1021/acs.jcim.4c00464","pmid":"https://pubmed.ncbi.nlm.nih.gov/39225694"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c00464","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00464","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":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11542680/pdf/nihms-2027946.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022365732","display_name":"Hsu\u2010Chun Tsai","orcid":"https://orcid.org/0000-0001-7027-5649"},"institutions":[{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]},{"id":"https://openalex.org/I4210103385","display_name":"Tandem Diabetes Care (United States)","ror":"https://ror.org/01mzspr34","country_code":"US","type":"company","lineage":["https://openalex.org/I4210103385"]},{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hsu-Chun Tsai","raw_affiliation_strings":["Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States","TandemAI, New York, New York 10036, United States"],"affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States","institution_ids":["https://openalex.org/I4210098931","https://openalex.org/I102322142"]},{"raw_affiliation_string":"TandemAI, New York, New York 10036, United States","institution_ids":["https://openalex.org/I4210103385"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109775911","display_name":"James Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210103385","display_name":"Tandem Diabetes Care (United States)","ror":"https://ror.org/01mzspr34","country_code":"US","type":"company","lineage":["https://openalex.org/I4210103385"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Xu","raw_affiliation_strings":["TandemAI, New York, New York 10036, United States"],"affiliations":[{"raw_affiliation_string":"TandemAI, New York, New York 10036, United States","institution_ids":["https://openalex.org/I4210103385"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101348222","display_name":"Guo Zhenyu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210103385","display_name":"Tandem Diabetes Care (United States)","ror":"https://ror.org/01mzspr34","country_code":"US","type":"company","lineage":["https://openalex.org/I4210103385"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhenyu Guo","raw_affiliation_strings":["TandemAI, New York, New York 10036, United States"],"affiliations":[{"raw_affiliation_string":"TandemAI, New York, New York 10036, United States","institution_ids":["https://openalex.org/I4210103385"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106982912","display_name":"Yinhui Yi","orcid":null},"institutions":[{"id":"https://openalex.org/I4210103385","display_name":"Tandem Diabetes Care (United States)","ror":"https://ror.org/01mzspr34","country_code":"US","type":"company","lineage":["https://openalex.org/I4210103385"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yinhui Yi","raw_affiliation_strings":["TandemAI, New York, New York 10036, United States"],"affiliations":[{"raw_affiliation_string":"TandemAI, New York, New York 10036, United States","institution_ids":["https://openalex.org/I4210103385"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008526650","display_name":"Chuan Tian","orcid":"https://orcid.org/0000-0002-3518-7237"},"institutions":[{"id":"https://openalex.org/I4210103385","display_name":"Tandem Diabetes Care (United States)","ror":"https://ror.org/01mzspr34","country_code":"US","type":"company","lineage":["https://openalex.org/I4210103385"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chuan Tian","raw_affiliation_strings":["TandemAI, New York, New York 10036, United States"],"affiliations":[{"raw_affiliation_string":"TandemAI, New York, New York 10036, United States","institution_ids":["https://openalex.org/I4210103385"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061975788","display_name":"Xinyu Que","orcid":"https://orcid.org/0000-0002-4057-3255"},"institutions":[{"id":"https://openalex.org/I4210103385","display_name":"Tandem Diabetes Care (United States)","ror":"https://ror.org/01mzspr34","country_code":"US","type":"company","lineage":["https://openalex.org/I4210103385"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xinyu Que","raw_affiliation_strings":["TandemAI, New York, New York 10036, United States"],"affiliations":[{"raw_affiliation_string":"TandemAI, New York, New York 10036, United States","institution_ids":["https://openalex.org/I4210103385"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007304685","display_name":"Timothy J. Giese","orcid":"https://orcid.org/0000-0002-0653-9168"},"institutions":[{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]},{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Timothy Giese","raw_affiliation_strings":["Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States"],"affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States","institution_ids":["https://openalex.org/I4210098931","https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029666960","display_name":"Tai\u2010Sung Lee","orcid":"https://orcid.org/0000-0003-2110-2279"},"institutions":[{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]},{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tai-Sung Lee","raw_affiliation_strings":["Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States"],"affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States","institution_ids":["https://openalex.org/I4210098931","https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076436548","display_name":"Darrin M. York","orcid":"https://orcid.org/0000-0002-9193-7055"},"institutions":[{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]},{"id":"https://openalex.org/I102322142","display_name":"Rutgers, The State University of New Jersey","ror":"https://ror.org/05vt9qd57","country_code":"US","type":"education","lineage":["https://openalex.org/I102322142"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Darrin M. York","raw_affiliation_strings":["Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States"],"affiliations":[{"raw_affiliation_string":"Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States","institution_ids":["https://openalex.org/I4210098931","https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030955730","display_name":"Abir Ganguly","orcid":"https://orcid.org/0000-0002-0630-1109"},"institutions":[{"id":"https://openalex.org/I4210103385","display_name":"Tandem Diabetes Care (United States)","ror":"https://ror.org/01mzspr34","country_code":"US","type":"company","lineage":["https://openalex.org/I4210103385"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Abir Ganguly","raw_affiliation_strings":["TandemAI, New York, New York 10036, United States"],"affiliations":[{"raw_affiliation_string":"TandemAI, New York, New York 10036, United States","institution_ids":["https://openalex.org/I4210103385"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076110000","display_name":"Albert C. Pan","orcid":"https://orcid.org/0000-0001-5050-5603"},"institutions":[{"id":"https://openalex.org/I4210103385","display_name":"Tandem Diabetes Care (United States)","ror":"https://ror.org/01mzspr34","country_code":"US","type":"company","lineage":["https://openalex.org/I4210103385"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Albert Pan","raw_affiliation_strings":["TandemAI, New York, New York 10036, United States"],"affiliations":[{"raw_affiliation_string":"TandemAI, New York, New York 10036, United States","institution_ids":["https://openalex.org/I4210103385"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5030955730","https://openalex.org/A5076110000","https://openalex.org/A5076436548"],"corresponding_institution_ids":["https://openalex.org/I102322142","https://openalex.org/I4210098931","https://openalex.org/I4210103385"],"apc_list":null,"apc_paid":null,"fwci":1.653,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.83845415,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"64","issue":"18","first_page":"7046","last_page":"7055"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9957000017166138,"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/T11936","display_name":"Chemical and Physical Properties in Aqueous Solutions","score":0.9891999959945679,"subfield":{"id":"https://openalex.org/subfields/1506","display_name":"Filtration and Separation"},"field":{"id":"https://openalex.org/fields/15","display_name":"Chemical Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/alchemy","display_name":"Alchemy","score":0.6961154937744141},{"id":"https://openalex.org/keywords/sampling","display_name":"Sampling (signal processing)","score":0.5820605158805847},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.49644309282302856},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.42723333835601807},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.40259188413619995},{"id":"https://openalex.org/keywords/environmental-science","display_name":"Environmental science","score":0.3713837265968323},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.31482332944869995},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.29422053694725037},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21444007754325867},{"id":"https://openalex.org/keywords/art","display_name":"Art","score":0.0800832211971283},{"id":"https://openalex.org/keywords/art-history","display_name":"Art history","score":0.06956923007965088}],"concepts":[{"id":"https://openalex.org/C174468945","wikidata":"https://www.wikidata.org/wiki/Q39689","display_name":"Alchemy","level":2,"score":0.6961154937744141},{"id":"https://openalex.org/C140779682","wikidata":"https://www.wikidata.org/wiki/Q210868","display_name":"Sampling (signal processing)","level":3,"score":0.5820605158805847},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.49644309282302856},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.42723333835601807},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.40259188413619995},{"id":"https://openalex.org/C39432304","wikidata":"https://www.wikidata.org/wiki/Q188847","display_name":"Environmental science","level":0,"score":0.3713837265968323},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.31482332944869995},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.29422053694725037},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21444007754325867},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0800832211971283},{"id":"https://openalex.org/C52119013","wikidata":"https://www.wikidata.org/wiki/Q50637","display_name":"Art history","level":1,"score":0.06956923007965088},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.0},{"id":"https://openalex.org/C106131492","wikidata":"https://www.wikidata.org/wiki/Q3072260","display_name":"Filter (signal processing)","level":2,"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":"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":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"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":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D054852","descriptor_name":"Small Molecule Libraries","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1021/acs.jcim.4c00464","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c00464","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:39225694","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39225694","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},{"id":"pmh:oai:pubmedcentral.nih.gov:11542680","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11542680/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11542680/pdf/nihms-2027946.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},{"id":"pmh:oai:europepmc.org:11259981","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11542680","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:11542680","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11542680/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11542680/pdf/nihms-2027946.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","score":0.8700000047683716,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G1433134892","display_name":null,"funder_award_id":"ACI-154856","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G1742171491","display_name":null,"funder_award_id":"1548562","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2206590661","display_name":null,"funder_award_id":"ACI-1548562","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3147773666","display_name":null,"funder_award_id":"ACI-1548562","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"},{"id":"https://openalex.org/G3355158854","display_name":null,"funder_award_id":"548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3376445288","display_name":null,"funder_award_id":"XSEDE","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"},{"id":"https://openalex.org/G367708065","display_name":null,"funder_award_id":"ACI-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3709464396","display_name":null,"funder_award_id":"-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3730782400","display_name":null,"funder_award_id":"1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G417905534","display_name":null,"funder_award_id":"XSEDE","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5687282607","display_name":null,"funder_award_id":"GM107485","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6345853531","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7260934811","display_name":null,"funder_award_id":"CI-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8907196067","display_name":null,"funder_award_id":"-1548562","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320316545","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337393","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4402206730.pdf"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W1594503666","https://openalex.org/W1969189143","https://openalex.org/W1973209866","https://openalex.org/W1976499671","https://openalex.org/W1984052581","https://openalex.org/W1984481443","https://openalex.org/W1984604072","https://openalex.org/W1993177346","https://openalex.org/W1993300454","https://openalex.org/W1997772366","https://openalex.org/W2011207690","https://openalex.org/W2021220203","https://openalex.org/W2025006523","https://openalex.org/W2035687084","https://openalex.org/W2040809566","https://openalex.org/W2042443692","https://openalex.org/W2043383571","https://openalex.org/W2060433756","https://openalex.org/W2065963893","https://openalex.org/W2067174909","https://openalex.org/W2083038332","https://openalex.org/W2089258285","https://openalex.org/W2091286894","https://openalex.org/W2091562724","https://openalex.org/W2103945336","https://openalex.org/W2104630281","https://openalex.org/W2106140689","https://openalex.org/W2120987099","https://openalex.org/W2121111513","https://openalex.org/W2132776121","https://openalex.org/W2146942655","https://openalex.org/W2147993766","https://openalex.org/W2149655632","https://openalex.org/W2154670681","https://openalex.org/W2155500030","https://openalex.org/W2156502139","https://openalex.org/W2173076998","https://openalex.org/W2313116527","https://openalex.org/W2326979787","https://openalex.org/W2730519791","https://openalex.org/W2784756177","https://openalex.org/W2786610377","https://openalex.org/W2800801983","https://openalex.org/W2891791233","https://openalex.org/W2908609756","https://openalex.org/W2912818999","https://openalex.org/W2956693404","https://openalex.org/W2982862739","https://openalex.org/W3029108182","https://openalex.org/W3047663514","https://openalex.org/W3049116538","https://openalex.org/W3087004338","https://openalex.org/W3090513030","https://openalex.org/W3103473131","https://openalex.org/W3111206976","https://openalex.org/W3125197509","https://openalex.org/W3126967313","https://openalex.org/W3166497653","https://openalex.org/W3167019654","https://openalex.org/W3188746092","https://openalex.org/W3201597079","https://openalex.org/W4200173198","https://openalex.org/W4207041243","https://openalex.org/W4221091810","https://openalex.org/W4221099386","https://openalex.org/W4285331314","https://openalex.org/W4293112991","https://openalex.org/W4310573576","https://openalex.org/W4313830069","https://openalex.org/W4315631931","https://openalex.org/W4385196378","https://openalex.org/W4387334097","https://openalex.org/W4387440676","https://openalex.org/W4395677718"],"related_works":["https://openalex.org/W2327690717","https://openalex.org/W1570968926","https://openalex.org/W2033179625","https://openalex.org/W2047294527","https://openalex.org/W4253737202","https://openalex.org/W2367275899","https://openalex.org/W599555033","https://openalex.org/W2502020699","https://openalex.org/W2500372171","https://openalex.org/W3107697994"],"abstract_inverted_index":{"Accurate":[0],"<i>in":[1],"silico</i>":[2],"predictions":[3],"of":[4,28,35,42,68,77,85,113,136,145,151],"how":[5,132],"strongly":[6],"small":[7,80,119],"molecules":[8,120],"bind":[9],"to":[10,87],"proteins,":[11],"such":[12,43],"as":[13],"those":[14],"afforded":[15],"by":[16,95,105],"relative":[17],"binding":[18],"free":[19],"energy":[20],"(RBFE)":[21],"calculations,":[22,44],"can":[23,63],"greatly":[24],"increase":[25],"the":[26,29,36,66,92,101,143],"efficiency":[27],"hit-to-lead":[30],"and":[31,74,79,100,117],"lead":[32],"optimization":[33],"stages":[34],"drug":[37],"discovery":[38],"process.":[39],"The":[40,83],"success":[41],"however,":[45],"relies":[46],"heavily":[47],"on":[48,71],"their":[49],"precision.":[50],"Here,":[51],"we":[52],"show":[53,128],"that":[54],"a":[55,72,111],"recently":[56],"developed":[57],"alchemical":[58],"enhanced":[59],"sampling":[60,144],"(ACES)":[61],"approach":[62],"consistently":[64],"improve":[65],"precision":[67],"RBFE":[69,89,139],"calculations":[70,90,140],"large":[73],"diverse":[75],"set":[76,112],"proteins":[78],"molecule":[81],"ligands.":[82],"addition":[84],"ACES":[86,133],"conventional":[88],"lowered":[91],"average":[93,102],"hysteresis":[94],"over":[96,106],"35%":[97],"(0.3-0.4":[98],"kcal/mol)":[99,109],"replicate":[103],"spread":[104],"25%":[107],"(0.2-0.3":[108],"across":[110],"10":[114],"protein":[115],"targets":[116],"213":[118],"while":[121],"maintaining":[122],"similar":[123],"or":[124],"improved":[125,134],"accuracy.":[126],"We":[127],"in":[129],"atomic":[130],"detail":[131],"convergence":[135],"several":[137],"representative":[138],"through":[141],"enhancing":[142],"important":[146],"slowly":[147],"transitioning":[148],"ligand":[149],"degrees":[150],"freedom.":[152]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5}],"updated_date":"2026-03-25T14:56:36.534964","created_date":"2025-10-10T00:00:00"}