{"id":"https://openalex.org/W3087004338","doi":"https://doi.org/10.1021/acs.jcim.0c00613","title":"Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery","display_name":"Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery","publication_year":2020,"publication_date":"2020-09-16","ids":{"openalex":"https://openalex.org/W3087004338","doi":"https://doi.org/10.1021/acs.jcim.0c00613","mag":"3087004338","pmid":"https://pubmed.ncbi.nlm.nih.gov/32936637"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c00613","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00613","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://www.ncbi.nlm.nih.gov/pmc/articles/7686026","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tai-Sung Lee","raw_affiliation_strings":["Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, New Brunswick, New Jersey 08901-8554, United States"],"affiliations":[{"raw_affiliation_string":"Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, New Brunswick, New Jersey 08901-8554, United States","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004009215","display_name":"Bryce K. Allen","orcid":"https://orcid.org/0000-0002-0804-8127"},"institutions":[{"id":"https://openalex.org/I4210094840","display_name":"Silicon Therapeutics (United States)","ror":"https://ror.org/00rbf3t83","country_code":"US","type":"company","lineage":["https://openalex.org/I4210094840"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bryce K. Allen","raw_affiliation_strings":["Silicon Therapeutics, Boston, Massachusetts 02210, United States"],"affiliations":[{"raw_affiliation_string":"Silicon Therapeutics, Boston, Massachusetts 02210, United States","institution_ids":["https://openalex.org/I4210094840"]}]},{"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/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 J. Giese","raw_affiliation_strings":["Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, New Brunswick, New Jersey 08901-8554, United States"],"affiliations":[{"raw_affiliation_string":"Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, New Brunswick, New Jersey 08901-8554, United States","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074075949","display_name":"Zhenyu Guo","orcid":"https://orcid.org/0000-0001-5595-6251"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhenyu Guo","raw_affiliation_strings":["Silicon Therapeutics, Suzhou, Jiansu, 215000, China"],"affiliations":[{"raw_affiliation_string":"Silicon Therapeutics, Suzhou, Jiansu, 215000, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100339736","display_name":"Pengfei Li","orcid":"https://orcid.org/0000-0001-9355-6371"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pengfei Li","raw_affiliation_strings":["Silicon Therapeutics, Suzhou, Jiansu, 215000, China"],"affiliations":[{"raw_affiliation_string":"Silicon Therapeutics, Suzhou, Jiansu, 215000, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091587653","display_name":"Charles Lin","orcid":"https://orcid.org/0000-0002-5461-6690"},"institutions":[{"id":"https://openalex.org/I4210094840","display_name":"Silicon Therapeutics (United States)","ror":"https://ror.org/00rbf3t83","country_code":"US","type":"company","lineage":["https://openalex.org/I4210094840"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Charles Lin","raw_affiliation_strings":["Silicon Therapeutics, Boston, Massachusetts 02210, United States"],"affiliations":[{"raw_affiliation_string":"Silicon Therapeutics, Boston, Massachusetts 02210, United States","institution_ids":["https://openalex.org/I4210094840"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049193748","display_name":"T. Dwight McGee","orcid":"https://orcid.org/0000-0003-2138-8385"},"institutions":[{"id":"https://openalex.org/I4210094840","display_name":"Silicon Therapeutics (United States)","ror":"https://ror.org/00rbf3t83","country_code":"US","type":"company","lineage":["https://openalex.org/I4210094840"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"T. Dwight McGee","raw_affiliation_strings":["Silicon Therapeutics, Boston, Massachusetts 02210, United States"],"affiliations":[{"raw_affiliation_string":"Silicon Therapeutics, Boston, Massachusetts 02210, United States","institution_ids":["https://openalex.org/I4210094840"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014464745","display_name":"David A. Pearlman","orcid":"https://orcid.org/0000-0002-2574-6066"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"David A. Pearlman","raw_affiliation_strings":["QSimulate Incorporated, Cambridge, Massachusetts 02139, United States"],"affiliations":[{"raw_affiliation_string":"QSimulate Incorporated, Cambridge, Massachusetts 02139, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089169254","display_name":"Brian K. Radak","orcid":"https://orcid.org/0000-0001-8628-5972"},"institutions":[{"id":"https://openalex.org/I4210094840","display_name":"Silicon Therapeutics (United States)","ror":"https://ror.org/00rbf3t83","country_code":"US","type":"company","lineage":["https://openalex.org/I4210094840"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Brian K. Radak","raw_affiliation_strings":["Silicon Therapeutics, Boston, Massachusetts 02210, United States"],"affiliations":[{"raw_affiliation_string":"Silicon Therapeutics, Boston, Massachusetts 02210, United States","institution_ids":["https://openalex.org/I4210094840"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015187080","display_name":"Yujun Tao","orcid":"https://orcid.org/0000-0002-4520-941X"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yujun Tao","raw_affiliation_strings":["Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, New Brunswick, New Jersey 08901-8554, United States"],"affiliations":[{"raw_affiliation_string":"Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, New Brunswick, New Jersey 08901-8554, United States","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022365732","display_name":"Hsu\u2010Chun Tsai","orcid":"https://orcid.org/0000-0001-7027-5649"},"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"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hsu-Chun Tsai","raw_affiliation_strings":["Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, New Brunswick, New Jersey 08901-8554, United States"],"affiliations":[{"raw_affiliation_string":"Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, New Brunswick, New Jersey 08901-8554, United States","institution_ids":["https://openalex.org/I102322142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019096017","display_name":"Huafeng Xu","orcid":"https://orcid.org/0000-0001-5447-0452"},"institutions":[{"id":"https://openalex.org/I4210094840","display_name":"Silicon Therapeutics (United States)","ror":"https://ror.org/00rbf3t83","country_code":"US","type":"company","lineage":["https://openalex.org/I4210094840"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Huafeng Xu","raw_affiliation_strings":["Silicon Therapeutics, Boston, Massachusetts 02210, United States"],"affiliations":[{"raw_affiliation_string":"Silicon Therapeutics, Boston, Massachusetts 02210, United States","institution_ids":["https://openalex.org/I4210094840"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087455853","display_name":"Woody Sherman","orcid":"https://orcid.org/0000-0001-9079-1376"},"institutions":[{"id":"https://openalex.org/I4210094840","display_name":"Silicon Therapeutics (United States)","ror":"https://ror.org/00rbf3t83","country_code":"US","type":"company","lineage":["https://openalex.org/I4210094840"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Woody Sherman","raw_affiliation_strings":["Silicon Therapeutics, Boston, Massachusetts 02210, United States"],"affiliations":[{"raw_affiliation_string":"Silicon Therapeutics, Boston, Massachusetts 02210, United States","institution_ids":["https://openalex.org/I4210094840"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076436548","display_name":"Darrin M. York","orcid":"https://orcid.org/0000-0002-9193-7055"},"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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Darrin M. York","raw_affiliation_strings":["Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, New Brunswick, New Jersey 08901-8554, United States"],"affiliations":[{"raw_affiliation_string":"Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, New Brunswick, New Jersey 08901-8554, United States","institution_ids":["https://openalex.org/I102322142"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":14,"corresponding_author_ids":["https://openalex.org/A5076436548","https://openalex.org/A5087455853"],"corresponding_institution_ids":["https://openalex.org/I102322142","https://openalex.org/I4210094840"],"apc_list":null,"apc_paid":null,"fwci":29.038,"has_fulltext":false,"cited_by_count":369,"citation_normalized_percentile":{"value":0.99760591,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"60","issue":"11","first_page":"5595","last_page":"5623"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9990000128746033,"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":0.9990000128746033,"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":0.9902999997138977,"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/T13013","display_name":"Free Radicals and Antioxidants","score":0.967199981212616,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"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/drug-discovery","display_name":"Drug discovery","score":0.7429871559143066},{"id":"https://openalex.org/keywords/alchemy","display_name":"Alchemy","score":0.6493132710456848},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.5150837302207947},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.4927842915058136},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4153684377670288},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4066125154495239},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3263792097568512},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.29438549280166626},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.24084016680717468},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.19141221046447754},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17430183291435242},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.17033877968788147},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.11825257539749146},{"id":"https://openalex.org/keywords/history","display_name":"History","score":0.11240020394325256},{"id":"https://openalex.org/keywords/art-history","display_name":"Art history","score":0.08103376626968384}],"concepts":[{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.7429871559143066},{"id":"https://openalex.org/C174468945","wikidata":"https://www.wikidata.org/wiki/Q39689","display_name":"Alchemy","level":2,"score":0.6493132710456848},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.5150837302207947},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.4927842915058136},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4153684377670288},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4066125154495239},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3263792097568512},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.29438549280166626},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.24084016680717468},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.19141221046447754},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17430183291435242},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.17033877968788147},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.11825257539749146},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.11240020394325256},{"id":"https://openalex.org/C52119013","wikidata":"https://www.wikidata.org/wiki/Q50637","display_name":"Art history","level":1,"score":0.08103376626968384}],"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":"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":"D011485","descriptor_name":"Protein Binding","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":"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},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","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":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","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":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.0c00613","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00613","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:32936637","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32936637","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:7686026","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7686026","pdf_url":null,"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"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7686026","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7686026","pdf_url":null,"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","display_name":"Affordable and clean energy","score":0.7599999904632568}],"awards":[{"id":"https://openalex.org/G6436539719","display_name":null,"funder_award_id":"GM107485","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":300,"referenced_works":["https://openalex.org/W141181845","https://openalex.org/W1034882992","https://openalex.org/W1178456644","https://openalex.org/W1522205938","https://openalex.org/W1569273074","https://openalex.org/W1587176568","https://openalex.org/W1602377520","https://openalex.org/W1625910593","https://openalex.org/W1677676180","https://openalex.org/W1785767033","https://openalex.org/W1932588580","https://openalex.org/W1964758803","https://openalex.org/W1967532320","https://openalex.org/W1968484323","https://openalex.org/W1969189143","https://openalex.org/W1969873373","https://openalex.org/W1969910482","https://openalex.org/W1970973025","https://openalex.org/W1971617876","https://openalex.org/W1972666382","https://openalex.org/W1973447651","https://openalex.org/W1975691556","https://openalex.org/W1976161355","https://openalex.org/W1976263218","https://openalex.org/W1977234725","https://openalex.org/W1978193721","https://openalex.org/W1978393297","https://openalex.org/W1981128082","https://openalex.org/W1983312705","https://openalex.org/W1983450159","https://openalex.org/W1983731524","https://openalex.org/W1984204835","https://openalex.org/W1984481443","https://openalex.org/W1986191025","https://openalex.org/W1986411697","https://openalex.org/W1987097510","https://openalex.org/W1989195611","https://openalex.org/W1989497142","https://openalex.org/W1992191950","https://openalex.org/W1992531741","https://openalex.org/W1993177346","https://openalex.org/W1993765343","https://openalex.org/W1995125384","https://openalex.org/W1995152253","https://openalex.org/W1997125900","https://openalex.org/W1997727027","https://openalex.org/W1997772366","https://openalex.org/W2000219995","https://openalex.org/W2001368885","https://openalex.org/W2002912579","https://openalex.org/W2003486716","https://openalex.org/W2004640547","https://openalex.org/W2004822259","https://openalex.org/W2005647584","https://openalex.org/W2007349244","https://openalex.org/W2009218781","https://openalex.org/W2009499526","https://openalex.org/W2009647460","https://openalex.org/W2010882262","https://openalex.org/W2012500759","https://openalex.org/W2013291622","https://openalex.org/W2013308479","https://openalex.org/W2013638918","https://openalex.org/W2014433873","https://openalex.org/W2015848270","https://openalex.org/W2017829285","https://openalex.org/W2018294192","https://openalex.org/W2019962781","https://openalex.org/W2020040806","https://openalex.org/W2020715558","https://openalex.org/W2021284440","https://openalex.org/W2021832765","https://openalex.org/W2024225780","https://openalex.org/W2024553805","https://openalex.org/W2024762727","https://openalex.org/W2025006523","https://openalex.org/W2027109368","https://openalex.org/W2029454849","https://openalex.org/W2029667189","https://openalex.org/W2029973510","https://openalex.org/W2031168104","https://openalex.org/W2032044839","https://openalex.org/W2032139608","https://openalex.org/W2035078255","https://openalex.org/W2035672721","https://openalex.org/W2035687084","https://openalex.org/W2036616433","https://openalex.org/W2037320233","https://openalex.org/W2037386768","https://openalex.org/W2038452296","https://openalex.org/W2039526577","https://openalex.org/W2041189078","https://openalex.org/W2041293484","https://openalex.org/W2041560550","https://openalex.org/W2042129725","https://openalex.org/W2042821667","https://openalex.org/W2042980919","https://openalex.org/W2043383571","https://openalex.org/W2043701535","https://openalex.org/W2044019273","https://openalex.org/W2044444984","https://openalex.org/W2048675518","https://openalex.org/W2049654081","https://openalex.org/W2050394034","https://openalex.org/W2050774715","https://openalex.org/W2051082589","https://openalex.org/W2051263598","https://openalex.org/W2051551120","https://openalex.org/W2058479011","https://openalex.org/W2060433756","https://openalex.org/W2063206968","https://openalex.org/W2063535987","https://openalex.org/W2063667373","https://openalex.org/W2065655440","https://openalex.org/W2065963893","https://openalex.org/W2066425873","https://openalex.org/W2066690664","https://openalex.org/W2066951434","https://openalex.org/W2067174909","https://openalex.org/W2067235926","https://openalex.org/W2070830937","https://openalex.org/W2071231667","https://openalex.org/W2072256473","https://openalex.org/W2072604508","https://openalex.org/W2074974429","https://openalex.org/W2075468840","https://openalex.org/W2075701764","https://openalex.org/W2075956726","https://openalex.org/W2076308231","https://openalex.org/W2078413200","https://openalex.org/W2079188379","https://openalex.org/W2079318633","https://openalex.org/W2081167734","https://openalex.org/W2081773466","https://openalex.org/W2081775931","https://openalex.org/W2083624153","https://openalex.org/W2084352399","https://openalex.org/W2088933990","https://openalex.org/W2090786343","https://openalex.org/W2092956715","https://openalex.org/W2093176297","https://openalex.org/W2093327248","https://openalex.org/W2093381148","https://openalex.org/W2093755925","https://openalex.org/W2094779443","https://openalex.org/W2094880882","https://openalex.org/W2099565782","https://openalex.org/W2104630281","https://openalex.org/W2107676206","https://openalex.org/W2111917512","https://openalex.org/W2113623846","https://openalex.org/W2114239896","https://openalex.org/W2117620409","https://openalex.org/W2120795798","https://openalex.org/W2124504636","https://openalex.org/W2125504256","https://openalex.org/W2131643298","https://openalex.org/W2132629607","https://openalex.org/W2132717858","https://openalex.org/W2140151763","https://openalex.org/W2140841928","https://openalex.org/W2144081223","https://openalex.org/W2144288821","https://openalex.org/W2144775933","https://openalex.org/W2145722722","https://openalex.org/W2146575889","https://openalex.org/W2146942655","https://openalex.org/W2147993766","https://openalex.org/W2149302140","https://openalex.org/W2149655632","https://openalex.org/W2149801992","https://openalex.org/W2150096023","https://openalex.org/W2150629485","https://openalex.org/W2150981663","https://openalex.org/W2152403153","https://openalex.org/W2154670681","https://openalex.org/W2154714625","https://openalex.org/W2155072429","https://openalex.org/W2155554859","https://openalex.org/W2155714626","https://openalex.org/W2156502139","https://openalex.org/W2159383649","https://openalex.org/W2162027701","https://openalex.org/W2162166182","https://openalex.org/W2164497185","https://openalex.org/W2167825723","https://openalex.org/W2168357118","https://openalex.org/W2169033132","https://openalex.org/W2171047927","https://openalex.org/W2228949267","https://openalex.org/W2262253939","https://openalex.org/W2278367844","https://openalex.org/W2290500375","https://openalex.org/W2295762426","https://openalex.org/W2296686360","https://openalex.org/W2312878509","https://openalex.org/W2313048821","https://openalex.org/W2313116527","https://openalex.org/W2314036509","https://openalex.org/W2314621752","https://openalex.org/W2327851360","https://openalex.org/W2329704667","https://openalex.org/W2330799739","https://openalex.org/W2331161041","https://openalex.org/W2334277474","https://openalex.org/W2337762266","https://openalex.org/W2338036129","https://openalex.org/W2340673380","https://openalex.org/W2344666683","https://openalex.org/W2404280981","https://openalex.org/W2404459885","https://openalex.org/W2407851381","https://openalex.org/W2416918185","https://openalex.org/W2463208053","https://openalex.org/W2471079269","https://openalex.org/W2480983928","https://openalex.org/W2512007918","https://openalex.org/W2552522590","https://openalex.org/W2561642182","https://openalex.org/W2562368273","https://openalex.org/W2570970768","https://openalex.org/W2582687887","https://openalex.org/W2593105084","https://openalex.org/W2593584634","https://openalex.org/W2599323046","https://openalex.org/W2604723280","https://openalex.org/W2607560340","https://openalex.org/W2613985600","https://openalex.org/W2616199713","https://openalex.org/W2621922190","https://openalex.org/W2623172571","https://openalex.org/W2625712932","https://openalex.org/W2718878673","https://openalex.org/W2730519791","https://openalex.org/W2749311864","https://openalex.org/W2755682685","https://openalex.org/W2757663759","https://openalex.org/W2772606519","https://openalex.org/W2778455315","https://openalex.org/W2784756177","https://openalex.org/W2784827262","https://openalex.org/W2788789259","https://openalex.org/W2791032147","https://openalex.org/W2801405255","https://openalex.org/W2805624422","https://openalex.org/W2807109642","https://openalex.org/W2807958710","https://openalex.org/W2883886126","https://openalex.org/W2885996170","https://openalex.org/W2891791233","https://openalex.org/W2895157296","https://openalex.org/W2895630903","https://openalex.org/W2896297247","https://openalex.org/W2896588574","https://openalex.org/W2896970029","https://openalex.org/W2899481329","https://openalex.org/W2904110477","https://openalex.org/W2908609756","https://openalex.org/W2912364028","https://openalex.org/W2912818999","https://openalex.org/W2913359477","https://openalex.org/W2914734959","https://openalex.org/W2915927413","https://openalex.org/W2921674955","https://openalex.org/W2946891612","https://openalex.org/W2949467224","https://openalex.org/W2956693404","https://openalex.org/W2967253501","https://openalex.org/W2972646529","https://openalex.org/W2979514608","https://openalex.org/W2981128300","https://openalex.org/W2981264174","https://openalex.org/W2985021042","https://openalex.org/W2989052455","https://openalex.org/W2990010612","https://openalex.org/W2996021258","https://openalex.org/W2999639376","https://openalex.org/W3004820987","https://openalex.org/W3008905875","https://openalex.org/W3024881218","https://openalex.org/W3027827456","https://openalex.org/W3027960450","https://openalex.org/W3030632407","https://openalex.org/W3034934060","https://openalex.org/W3036448122","https://openalex.org/W3042009478","https://openalex.org/W3043456144","https://openalex.org/W3044187902","https://openalex.org/W3087352249","https://openalex.org/W3099180995","https://openalex.org/W3102529165","https://openalex.org/W3102805951","https://openalex.org/W3103473131","https://openalex.org/W3104005636","https://openalex.org/W3105581675","https://openalex.org/W3105643282","https://openalex.org/W3151633358","https://openalex.org/W3205656430","https://openalex.org/W4235673852","https://openalex.org/W4250719744"],"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/W2013003323","https://openalex.org/W1981076832","https://openalex.org/W2024773645","https://openalex.org/W2001717001","https://openalex.org/W2043147644"],"abstract_inverted_index":{"Predicting":[0],"protein-ligand":[1],"binding":[2,109,133,145],"affinities":[3],"and":[4,27,82,105,159,199,205,221],"the":[5,36,68,72,95,123,167,185,190,196,218],"associated":[6,171,224],"thermodynamics":[7],"of":[8,15,67,94,107,122,189,217],"biomolecular":[9],"recognition":[10],"is":[11,210],"a":[12,24,86,129,214,233],"primary":[13],"objective":[14],"structure-based":[16],"drug":[17,60,115,237],"design.":[18],"Alchemical":[19],"free":[20,47,110,134,146],"energy":[21,48,111,135,147],"simulations":[22,49,112,229],"offer":[23],"highly":[25],"accurate":[26,204],"computationally":[28,141],"efficient":[29],"route":[30],"to":[31,101,157,202,212],"achieving":[32],"this":[33],"goal.":[34],"While":[35],"AMBER":[37,73],"molecular":[38],"dynamics":[39],"package":[40],"has":[41,63],"successfully":[42],"been":[43,64],"used":[44],"for":[45,54,181],"alchemical":[46,74,108,132,175,191],"in":[50,58,79,113,126,162,230],"academic":[51],"research":[52],"groups":[53],"decades,":[55],"widespread":[56],"impact":[57],"industrial":[59,114],"discovery":[61,116,238],"settings":[62],"minimal":[65],"because":[66],"previous":[69,96],"limitations":[70,97],"within":[71],"code,":[75],"coupled":[76],"with":[77,98,128,172,179,225,232],"challenges":[78],"system":[80],"setup":[81],"postprocessing":[83],"workflows.":[84],"Through":[85],"close":[87],"academia-industry":[88],"collaboration":[89],"we":[90,119,164],"have":[91],"addressed":[92],"many":[93],"an":[99],"aim":[100],"improve":[102],"accuracy,":[103],"efficiency,":[104],"robustness":[106],"applications.":[117,239],"Here,":[118],"highlight":[120],"some":[121],"recent":[124],"advances":[125,161],"AMBER20":[127],"focus":[130,234],"on":[131,235],"(BFE)":[136],"calculations,":[137,177],"which":[138],"are":[139,153],"less":[140],"intensive":[142],"than":[143],"alternative":[144],"methods":[148],"where":[149],"full":[150],"binding/unbinding":[151],"paths":[152],"explored.":[154],"In":[155],"addition":[156],"scientific":[158],"technical":[160],"AMBER20,":[163,231],"also":[165,195],"describe":[166],"essential":[168],"practical":[169,222],"aspects":[170],"running":[173,226],"relative":[174,227],"BFE":[176,228],"along":[178],"recommendations":[180],"best":[182],"practices,":[183],"highlighting":[184],"importance":[186],"not":[187],"only":[188],"simulation":[192],"code":[193],"but":[194],"auxiliary":[197],"functionalities":[198],"expertise":[200],"required":[201],"obtain":[203],"reliable":[206],"results.":[207],"This":[208],"work":[209],"intended":[211],"provide":[213],"contemporary":[215],"overview":[216],"scientific,":[219],"technical,":[220],"issues":[223],"real-world":[236]},"counts_by_year":[{"year":2026,"cited_by_count":19},{"year":2025,"cited_by_count":73},{"year":2024,"cited_by_count":76},{"year":2023,"cited_by_count":76},{"year":2022,"cited_by_count":67},{"year":2021,"cited_by_count":52},{"year":2020,"cited_by_count":6}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
