{"id":"https://openalex.org/W3080583403","doi":"https://doi.org/10.1021/acs.jcim.0c00547","title":"Evolution of Alchemical Free Energy Methods in Drug Discovery","display_name":"Evolution of Alchemical Free Energy Methods in Drug Discovery","publication_year":2020,"publication_date":"2020-08-20","ids":{"openalex":"https://openalex.org/W3080583403","doi":"https://doi.org/10.1021/acs.jcim.0c00547","mag":"3080583403","pmid":"https://pubmed.ncbi.nlm.nih.gov/32818371"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c00547","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00547","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/A5044114823","display_name":"Lin Frank Song","orcid":"https://orcid.org/0000-0002-1854-5215"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lin Frank Song","raw_affiliation_strings":["Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States"],"raw_orcid":"https://orcid.org/0000-0002-1854-5215","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085994852","display_name":"Kenneth M. Merz","orcid":"https://orcid.org/0000-0001-9139-5893"},"institutions":[{"id":"https://openalex.org/I87216513","display_name":"Michigan State University","ror":"https://ror.org/05hs6h993","country_code":"US","type":"education","lineage":["https://openalex.org/I87216513"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kenneth M. Merz","raw_affiliation_strings":["Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States"],"raw_orcid":"https://orcid.org/0000-0001-9139-5893","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States","institution_ids":["https://openalex.org/I87216513"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5085994852"],"corresponding_institution_ids":["https://openalex.org/I87216513"],"apc_list":null,"apc_paid":null,"fwci":5.3352,"has_fulltext":false,"cited_by_count":122,"citation_normalized_percentile":{"value":0.96832233,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"60","issue":"11","first_page":"5308","last_page":"5318"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/timeline","display_name":"Timeline","score":0.7345186471939087},{"id":"https://openalex.org/keywords/trace","display_name":"TRACE (psycholinguistics)","score":0.7144671678543091},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.7015314102172852},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6801685094833374},{"id":"https://openalex.org/keywords/extant-taxon","display_name":"Extant taxon","score":0.65015709400177},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5346276760101318},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.5233830213546753},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.5104309916496277},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4591812789440155},{"id":"https://openalex.org/keywords/work","display_name":"Work (physics)","score":0.41999104619026184},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.13068661093711853},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13017889857292175},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1028757393360138},{"id":"https://openalex.org/keywords/mechanical-engineering","display_name":"Mechanical engineering","score":0.09872081875801086},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.09776043891906738},{"id":"https://openalex.org/keywords/computer-security","display_name":"Computer security","score":0.0774054229259491}],"concepts":[{"id":"https://openalex.org/C4438859","wikidata":"https://www.wikidata.org/wiki/Q186117","display_name":"Timeline","level":2,"score":0.7345186471939087},{"id":"https://openalex.org/C75291252","wikidata":"https://www.wikidata.org/wiki/Q1315756","display_name":"TRACE (psycholinguistics)","level":2,"score":0.7144671678543091},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.7015314102172852},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6801685094833374},{"id":"https://openalex.org/C178300618","wikidata":"https://www.wikidata.org/wiki/Q1898509","display_name":"Extant taxon","level":2,"score":0.65015709400177},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5346276760101318},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.5233830213546753},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.5104309916496277},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4591812789440155},{"id":"https://openalex.org/C18762648","wikidata":"https://www.wikidata.org/wiki/Q42213","display_name":"Work (physics)","level":2,"score":0.41999104619026184},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.13068661093711853},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13017889857292175},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1028757393360138},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.09872081875801086},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.09776043891906738},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0774054229259491},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","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":"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":"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}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.0c00547","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00547","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:32818371","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32818371","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","score":0.8399999737739563,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G2957538862","display_name":null,"funder_award_id":"GM130641","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":162,"referenced_works":["https://openalex.org/W185137928","https://openalex.org/W193664518","https://openalex.org/W343086395","https://openalex.org/W1491824558","https://openalex.org/W1518747218","https://openalex.org/W1532494422","https://openalex.org/W1556106311","https://openalex.org/W1608506719","https://openalex.org/W1625910593","https://openalex.org/W1910508441","https://openalex.org/W1968078495","https://openalex.org/W1968484323","https://openalex.org/W1970111528","https://openalex.org/W1970973025","https://openalex.org/W1971565686","https://openalex.org/W1972361027","https://openalex.org/W1974336924","https://openalex.org/W1976469638","https://openalex.org/W1976499671","https://openalex.org/W1976870460","https://openalex.org/W1979046104","https://openalex.org/W1980292953","https://openalex.org/W1981907708","https://openalex.org/W1984481443","https://openalex.org/W1985510130","https://openalex.org/W1985550898","https://openalex.org/W1986508321","https://openalex.org/W1990914937","https://openalex.org/W1993299482","https://openalex.org/W1995152253","https://openalex.org/W1998948060","https://openalex.org/W1999245179","https://openalex.org/W1999283300","https://openalex.org/W1999916825","https://openalex.org/W2000523594","https://openalex.org/W2001150554","https://openalex.org/W2002253870","https://openalex.org/W2002268576","https://openalex.org/W2002664623","https://openalex.org/W2009987871","https://openalex.org/W2014060139","https://openalex.org/W2017251721","https://openalex.org/W2017829285","https://openalex.org/W2019962781","https://openalex.org/W2023585673","https://openalex.org/W2024762727","https://openalex.org/W2027952509","https://openalex.org/W2028841370","https://openalex.org/W2029058787","https://openalex.org/W2031107710","https://openalex.org/W2035266068","https://openalex.org/W2035432821","https://openalex.org/W2035672721","https://openalex.org/W2036250557","https://openalex.org/W2039665613","https://openalex.org/W2041189078","https://openalex.org/W2041791898","https://openalex.org/W2043383571","https://openalex.org/W2043429268","https://openalex.org/W2043592573","https://openalex.org/W2043668344","https://openalex.org/W2046681877","https://openalex.org/W2047730466","https://openalex.org/W2049475242","https://openalex.org/W2050226017","https://openalex.org/W2050774715","https://openalex.org/W2051203581","https://openalex.org/W2051381895","https://openalex.org/W2053248230","https://openalex.org/W2053379287","https://openalex.org/W2053858804","https://openalex.org/W2056516302","https://openalex.org/W2056760934","https://openalex.org/W2057593004","https://openalex.org/W2063206968","https://openalex.org/W2064776185","https://openalex.org/W2065294654","https://openalex.org/W2066677535","https://openalex.org/W2068077377","https://openalex.org/W2070753604","https://openalex.org/W2072256473","https://openalex.org/W2072604508","https://openalex.org/W2073714240","https://openalex.org/W2075093176","https://openalex.org/W2075468840","https://openalex.org/W2075701764","https://openalex.org/W2077125698","https://openalex.org/W2079199763","https://openalex.org/W2079318633","https://openalex.org/W2079769193","https://openalex.org/W2081167734","https://openalex.org/W2081926166","https://openalex.org/W2082433219","https://openalex.org/W2083624153","https://openalex.org/W2091778154","https://openalex.org/W2092178115","https://openalex.org/W2092956715","https://openalex.org/W2093278667","https://openalex.org/W2093327248","https://openalex.org/W2093755925","https://openalex.org/W2094779443","https://openalex.org/W2104630281","https://openalex.org/W2106140689","https://openalex.org/W2124060532","https://openalex.org/W2139447954","https://openalex.org/W2140151763","https://openalex.org/W2143752207","https://openalex.org/W2144062946","https://openalex.org/W2146942655","https://openalex.org/W2147421370","https://openalex.org/W2147993766","https://openalex.org/W2149989728","https://openalex.org/W2154670681","https://openalex.org/W2155524113","https://openalex.org/W2158542478","https://openalex.org/W2159010139","https://openalex.org/W2159383649","https://openalex.org/W2160733446","https://openalex.org/W2162166182","https://openalex.org/W2171787690","https://openalex.org/W2173076998","https://openalex.org/W2222589778","https://openalex.org/W2277530386","https://openalex.org/W2319057313","https://openalex.org/W2320656688","https://openalex.org/W2321484219","https://openalex.org/W2323257235","https://openalex.org/W2397139855","https://openalex.org/W2408820472","https://openalex.org/W2411580022","https://openalex.org/W2495659538","https://openalex.org/W2573266977","https://openalex.org/W2587433164","https://openalex.org/W2587480998","https://openalex.org/W2606142660","https://openalex.org/W2607560340","https://openalex.org/W2625712932","https://openalex.org/W2730519791","https://openalex.org/W2768709305","https://openalex.org/W2772606519","https://openalex.org/W2786610377","https://openalex.org/W2891791233","https://openalex.org/W2895630903","https://openalex.org/W2898021236","https://openalex.org/W2912818999","https://openalex.org/W2914938805","https://openalex.org/W2917738346","https://openalex.org/W2949467224","https://openalex.org/W2970207814","https://openalex.org/W2990010612","https://openalex.org/W3004098428","https://openalex.org/W3004448761","https://openalex.org/W3005452978","https://openalex.org/W3006105074","https://openalex.org/W3008905875","https://openalex.org/W3027827456","https://openalex.org/W3054319032","https://openalex.org/W3101006260","https://openalex.org/W3105581675","https://openalex.org/W3202257501","https://openalex.org/W4233702469","https://openalex.org/W4235537161"],"related_works":["https://openalex.org/W1858249912","https://openalex.org/W2114034199","https://openalex.org/W4391249598","https://openalex.org/W2317428717","https://openalex.org/W2734259032","https://openalex.org/W3094038556","https://openalex.org/W2014772881","https://openalex.org/W4254228154","https://openalex.org/W3049477255","https://openalex.org/W4296345146"],"abstract_inverted_index":{"The":[0],"goal":[1],"of":[2,17,85,133],"the":[3,10,15,37,67,83,135,145],"present":[4],"manuscript":[5],"is":[6,32],"to":[7,28,91,144],"succinctly":[8],"trace":[9],"key":[11],"technological":[12],"steps":[13],"in":[14,36,58,82,129,138],"evolution":[16],"alchemical":[18],"free":[19,49,73,104],"energy":[20,50,74,105],"methods":[21],"(AFEMs)":[22],"from":[23,113],"a":[24,29,93,130],"purely":[25],"theoretical":[26,97],"construct":[27],"method":[30],"that":[31,149],"now":[33],"widely":[34],"used":[35],"biotechnological":[38],"and":[39,119],"pharmaceutical":[40],"industries.":[41],"More":[42],"specifically,":[43],"we":[44,120],"focus":[45],"on":[46,117],"relative":[47],"binding":[48,72],"(RBFE)":[51],"computations":[52],"which":[53],"are":[54,142,150],"more":[55,68],"routinely":[56],"applied":[57],"computer":[59],"aided":[60],"drug":[61],"design":[62],"(CADD)":[63],"campaigns":[64],"rather":[65,89],"than":[66],"computationally":[69],"intensive":[70],"absolute":[71],"(ABFE)":[75],"computations.":[76],"We":[77],"have":[78],"not":[79],"been":[80],"exhaustive":[81],"development":[84],"our":[86],"timeline":[87],"but":[88],"try":[90],"weave":[92],"story":[94],"about":[95],"how":[96],"ideas":[98],"were":[99],"ultimately":[100],"converted":[101],"into":[102],"contemporary":[103],"capabilities.":[106],"Necessarily":[107],"this":[108,123,139],"story-telling":[109],"approach":[110],"limits":[111],"us":[112],"citing":[114],"all":[115,134],"work":[116,136],"AFEMs,":[118],"apologize":[121],"for":[122,126],"shortcoming.":[124],"However,":[125],"those":[127],"interested":[128],"broad":[131],"delineation":[132],"done":[137],"area":[140],"they":[141],"directed":[143],"many":[146],"excellent":[147],"reviews":[148],"extant.":[151]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":25},{"year":2024,"cited_by_count":31},{"year":2023,"cited_by_count":20},{"year":2022,"cited_by_count":20},{"year":2021,"cited_by_count":21},{"year":2020,"cited_by_count":3}],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2025-10-10T00:00:00"}
