{"id":"https://openalex.org/W2549686806","doi":"https://doi.org/10.1021/acs.jcim.6b00362","title":"Relative Binding Free Energy Calculations Applied to Protein Homology Models","display_name":"Relative Binding Free Energy Calculations Applied to Protein Homology Models","publication_year":2016,"publication_date":"2016-11-08","ids":{"openalex":"https://openalex.org/W2549686806","doi":"https://doi.org/10.1021/acs.jcim.6b00362","mag":"2549686806","pmid":"https://pubmed.ncbi.nlm.nih.gov/28024402"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.6b00362","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00362","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/A5088727374","display_name":"Daniel Cappel","orcid":"https://orcid.org/0000-0002-8460-7867"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Daniel Cappel","raw_affiliation_strings":["Schr\u00f6dinger GmbH, Dynamostra\u00dfe\r13, 68165 Mannheim, Germany"],"raw_orcid":"https://orcid.org/0000-0002-8460-7867","affiliations":[{"raw_affiliation_string":"Schr\u00f6dinger GmbH, Dynamostra\u00dfe\r13, 68165 Mannheim, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021965086","display_name":"Michelle Lynn Hall","orcid":null},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michelle Lynn Hall","raw_affiliation_strings":["Schrodinger Inc., 120 W 45th Street, New York, New York 10036, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Schrodinger Inc., 120 W 45th Street, New York, New York 10036, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059420065","display_name":"Eelke B. Lenselink","orcid":"https://orcid.org/0000-0001-5459-2978"},"institutions":[{"id":"https://openalex.org/I121797337","display_name":"Leiden University","ror":"https://ror.org/027bh9e22","country_code":"NL","type":"education","lineage":["https://openalex.org/I121797337"]},{"id":"https://openalex.org/I4210133171","display_name":"Centre for Human Drug Research","ror":"https://ror.org/044hshx49","country_code":"NL","type":"facility","lineage":["https://openalex.org/I4210133171"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Eelke B. Lenselink","raw_affiliation_strings":["Division\rof Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division\rof Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands","institution_ids":["https://openalex.org/I4210133171","https://openalex.org/I121797337"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037007489","display_name":"Thijs Beuming","orcid":"https://orcid.org/0000-0002-5991-7118"},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thijs Beuming","raw_affiliation_strings":["Schrodinger Inc., 120 W 45th Street, New York, New York 10036, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Schrodinger Inc., 120 W 45th Street, New York, New York 10036, United States","institution_ids":["https://openalex.org/I203455613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072926885","display_name":"Jun Qi","orcid":"https://orcid.org/0000-0002-1461-3356"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jun Qi","raw_affiliation_strings":["Department\rof Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 360 Longwood Avenue, LC-2210, Boston, Massachusetts 02215, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 360 Longwood Avenue, LC-2210, Boston, Massachusetts 02215, United States","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110274677","display_name":"James E. Bradner","orcid":null},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Bradner","raw_affiliation_strings":["Department\rof Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 360 Longwood Avenue, LC-2210, Boston, Massachusetts 02215, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 360 Longwood Avenue, LC-2210, Boston, Massachusetts 02215, United States","institution_ids":["https://openalex.org/I4210117453","https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087455853","display_name":"Woody Sherman","orcid":"https://orcid.org/0000-0001-9079-1376"},"institutions":[{"id":"https://openalex.org/I203455613","display_name":"Schrodinger (United States)","ror":"https://ror.org/05a3z6914","country_code":"US","type":"company","lineage":["https://openalex.org/I203455613"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Woody Sherman","raw_affiliation_strings":["Schrodinger Inc., 120 W 45th Street, New York, New York 10036, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Schrodinger Inc., 120 W 45th Street, New York, New York 10036, United States","institution_ids":["https://openalex.org/I203455613"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":4.0047,"has_fulltext":false,"cited_by_count":76,"citation_normalized_percentile":{"value":0.94124173,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"56","issue":"12","first_page":"2388","last_page":"2400"},"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":0.9984999895095825,"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/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9969000220298767,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4481222331523895},{"id":"https://openalex.org/keywords/homology-modeling","display_name":"Homology modeling","score":0.44458407163619995},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.41590675711631775},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3978908956050873},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25962725281715393},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2109283208847046},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.08937451243400574}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4481222331523895},{"id":"https://openalex.org/C169627665","wikidata":"https://www.wikidata.org/wiki/Q5767913","display_name":"Homology modeling","level":3,"score":0.44458407163619995},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.41590675711631775},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3978908956050873},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25962725281715393},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2109283208847046},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.08937451243400574},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"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":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017076","descriptor_name":"Computer-Aided Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017076","descriptor_name":"Computer-Aided Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017076","descriptor_name":"Computer-Aided Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017076","descriptor_name":"Computer-Aided Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040681","descriptor_name":"Structural Homology, Protein","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":3,"locations":[{"id":"doi:10.1021/acs.jcim.6b00362","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.6b00362","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:28024402","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28024402","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:europepmc.org:4685777","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5777225","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":null,"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.49000000953674316}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":72,"referenced_works":["https://openalex.org/W1566256344","https://openalex.org/W1587176568","https://openalex.org/W1601928101","https://openalex.org/W1625910593","https://openalex.org/W1964245683","https://openalex.org/W1966164805","https://openalex.org/W1973209866","https://openalex.org/W1974734322","https://openalex.org/W1975691556","https://openalex.org/W1980285986","https://openalex.org/W1980618423","https://openalex.org/W1984481443","https://openalex.org/W1985588649","https://openalex.org/W1987275960","https://openalex.org/W1990724722","https://openalex.org/W1992100298","https://openalex.org/W1998166222","https://openalex.org/W2004124673","https://openalex.org/W2005273025","https://openalex.org/W2009423060","https://openalex.org/W2009529127","https://openalex.org/W2010875534","https://openalex.org/W2014060139","https://openalex.org/W2021750784","https://openalex.org/W2025006523","https://openalex.org/W2027279463","https://openalex.org/W2027423337","https://openalex.org/W2028835439","https://openalex.org/W2031101869","https://openalex.org/W2031168104","https://openalex.org/W2032044839","https://openalex.org/W2041535798","https://openalex.org/W2043383571","https://openalex.org/W2043592573","https://openalex.org/W2046274153","https://openalex.org/W2046681877","https://openalex.org/W2048524630","https://openalex.org/W2051551120","https://openalex.org/W2060002448","https://openalex.org/W2063206968","https://openalex.org/W2066787645","https://openalex.org/W2073110681","https://openalex.org/W2076308231","https://openalex.org/W2083262282","https://openalex.org/W2091562724","https://openalex.org/W2094162409","https://openalex.org/W2097775366","https://openalex.org/W2103034037","https://openalex.org/W2106383417","https://openalex.org/W2114819818","https://openalex.org/W2124060532","https://openalex.org/W2128494768","https://openalex.org/W2129153475","https://openalex.org/W2130479394","https://openalex.org/W2132776121","https://openalex.org/W2140247386","https://openalex.org/W2140714126","https://openalex.org/W2142820798","https://openalex.org/W2143422060","https://openalex.org/W2146942655","https://openalex.org/W2154670681","https://openalex.org/W2160807621","https://openalex.org/W2171787690","https://openalex.org/W2222589778","https://openalex.org/W2285844360","https://openalex.org/W2321294576","https://openalex.org/W2323942455","https://openalex.org/W2346012195","https://openalex.org/W2346117320","https://openalex.org/W2404459885","https://openalex.org/W2416918185","https://openalex.org/W2511847589"],"related_works":["https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W3100946526","https://openalex.org/W3097199166","https://openalex.org/W3205476627","https://openalex.org/W2404148701","https://openalex.org/W3093512008","https://openalex.org/W3130075881","https://openalex.org/W1994793165"],"abstract_inverted_index":{"A":[0],"significant":[1],"challenge":[2],"and":[3,55,75,94,105,195,211,217,293,320],"potential":[4],"high-value":[5],"application":[6,299],"of":[7,15,47,52,58,62,102,126,156,158,171,239,284,300,317],"computer-aided":[8],"drug":[9,138,161],"design":[10],"is":[11,28,133,225],"the":[12,30,43,48,53,59,65,106,127,143,154,220,231,240,246,254,258,264,270,277,282,297,315,318,321],"accurate":[13,36],"prediction":[14],"protein\u2013ligand":[16],"binding":[17,37,179],"affinities.":[18],"Free":[19],"energy":[20,39],"perturbation":[21],"(FEP)":[22],"using":[23,207,222,234,285],"molecular":[24,259],"dynamics":[25,260],"(MD)":[26],"sampling":[27,73,256],"among":[29],"most":[31],"suitable":[32],"approaches":[33],"to":[34,42,91,108,145,180,242,253,267,269,302,312],"achieve":[35],"free":[38],"predictions,":[40],"due":[41],"rigorous":[44],"statistical":[45],"framework":[46],"methodology,":[49],"correct":[50],"representation":[51],"energetics,":[54],"thorough":[56],"treatment":[57],"important":[60],"degrees":[61],"freedom":[63],"in":[64,72,82,137,160,245,257,276],"system":[66,291],"(including":[67],"explicit":[68],"waters).":[69],"Recent":[70],"advances":[71],"methods":[74,288],"force":[76],"fields":[77],"coupled":[78],"with":[79,122,230,289],"vast":[80],"increases":[81],"computational":[83],"resources":[84],"have":[85,118],"made":[86],"FEP":[87,116,147,159,301,324],"a":[88,168,184,191,196,228],"viable":[89],"technology":[90],"drive":[92],"hit-to-lead":[93],"lead":[95],"optimization,":[96],"allowing":[97],"for":[98,273,296],"more":[99],"efficient":[100],"cycles":[101],"medicinal":[103],"chemistry":[104],"possibility":[107],"explore":[109],"much":[110],"larger":[111],"chemical":[112],"spaces.":[113],"However,":[114],"previous":[115],"applications":[117],"focused":[119],"on":[120,148,175,227],"systems":[121],"high-resolution":[123],"crystal":[124,209,235],"structures":[125,210],"target":[128],"as":[129,214],"starting":[130,215],"points\u2014something":[131],"that":[132,219],"not":[134],"always":[135],"available":[136],"discovery":[139],"projects.":[140],"As":[141],"such,":[142],"ability":[144],"apply":[146,167,205],"homology":[149,212,223,303],"models":[150,213,224,248],"would":[151],"greatly":[152],"expand":[153],"domain":[155],"applicability":[157],"discovery.":[162],"In":[163],"this":[164],"work":[165,280,326],"we":[166],"particular":[169],"implementation":[170],"FEP,":[172],"called":[173],"FEP+,":[174],"congeneric":[176],"ligand":[177,275],"series":[178],"four":[181],"diverse":[182],"targets:":[183],"kinase":[185],"(Tyk2),":[186],"an":[187],"epigenetic":[188],"bromodomain":[189],"(BRD4),":[190],"transmembrane":[192],"GPCR":[193],"(A2A),":[194],"protein\u2013protein":[197],"interaction":[198],"interface":[199],"(BCL-2":[200],"family":[201],"protein":[202],"MCL-1).":[203],"We":[204],"FEP+":[206],"both":[208],"points":[216],"find":[218],"performance":[221],"generally":[226],"par":[229],"results":[232],"when":[233],"structures.":[236],"The":[237],"robustness":[238],"calculations":[241],"structural":[243],"variations":[244],"input":[247],"can":[249],"likely":[250],"be":[251,310],"attributed":[252],"conformational":[255],"simulations,":[261],"which":[262],"allows":[263],"modeled":[265],"receptor":[266],"adapt":[268],"\u201creal\u201d":[271],"conformation":[272],"each":[274],"series.":[278],"This":[279],"exemplifies":[281],"advantages":[283],"all-atom":[286],"simulation":[287],"full":[290],"flexibility":[292],"offers":[294],"promise":[295],"general":[298],"models,":[304],"although":[305],"additional":[306],"validation":[307],"studies":[308],"should":[309],"performed":[311],"further":[313],"understand":[314],"limitations":[316],"method":[319],"scenarios":[322],"where":[323],"will":[325],"best.":[327]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
