{"id":"https://openalex.org/W4313312178","doi":"https://doi.org/10.1021/acs.jcim.2c01076","title":"An Open Source Graph-Based Weighted Cycle Closure Method for Relative Binding Free Energy Calculations","display_name":"An Open Source Graph-Based Weighted Cycle Closure Method for Relative Binding Free Energy Calculations","publication_year":2022,"publication_date":"2022-12-30","ids":{"openalex":"https://openalex.org/W4313312178","doi":"https://doi.org/10.1021/acs.jcim.2c01076","pmid":"https://pubmed.ncbi.nlm.nih.gov/36583975"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.2c01076","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01076","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/A5014352028","display_name":"Yishui Li","orcid":null},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yishui Li","raw_affiliation_strings":["Laboratory of Software Engineering for Complex System, National University of Defense Technology, Changsha410073, Hunan, P.R. China","Science and Technology on Parallel and Distributed Processing Laboratory, National University of Defense Technology, Changsha410073, Hunan, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Software Engineering for Complex System, National University of Defense Technology, Changsha410073, Hunan, P.R. China","institution_ids":["https://openalex.org/I170215575"]},{"raw_affiliation_string":"Science and Technology on Parallel and Distributed Processing Laboratory, National University of Defense Technology, Changsha410073, Hunan, P.R. China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080915850","display_name":"Runduo Liu","orcid":"https://orcid.org/0000-0002-8446-0404"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Runduo Liu","raw_affiliation_strings":["School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou510275, Guangdong, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou510275, Guangdong, P.R. China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100454196","display_name":"Jie Liu","orcid":"https://orcid.org/0000-0003-2046-3021"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Liu","raw_affiliation_strings":["Laboratory of Software Engineering for Complex System, National University of Defense Technology, Changsha410073, Hunan, P.R. China","Science and Technology on Parallel and Distributed Processing Laboratory, National University of Defense Technology, Changsha410073, Hunan, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Software Engineering for Complex System, National University of Defense Technology, Changsha410073, Hunan, P.R. China","institution_ids":["https://openalex.org/I170215575"]},{"raw_affiliation_string":"Science and Technology on Parallel and Distributed Processing Laboratory, National University of Defense Technology, Changsha410073, Hunan, P.R. China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Haibin Luo","orcid":null},"institutions":[{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haibin Luo","raw_affiliation_strings":["Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou570228, Hainan, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou570228, Hainan, P.R. China","institution_ids":["https://openalex.org/I20942203"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054335730","display_name":"Chengkun Wu","orcid":"https://orcid.org/0000-0002-9688-5311"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chengkun Wu","raw_affiliation_strings":["State Key Laboratory of High-Performance Computing, National University of Defense Technology, Changsha410073, Hunan, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of High-Performance Computing, National University of Defense Technology, Changsha410073, Hunan, P.R. China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100356685","display_name":"Zhe Li","orcid":"https://orcid.org/0000-0002-9357-6839"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhe Li","raw_affiliation_strings":["School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou510275, Guangdong, P.R. China"],"raw_orcid":"https://orcid.org/0000-0002-9357-6839","affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou510275, Guangdong, P.R. China","institution_ids":["https://openalex.org/I157773358"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5054335730","https://openalex.org/A5100356685"],"corresponding_institution_ids":["https://openalex.org/I157773358","https://openalex.org/I170215575"],"apc_list":null,"apc_paid":null,"fwci":1.0073,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.74817805,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"63","issue":"2","first_page":"561","last_page":"570"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9993000030517578,"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":0.9993000030517578,"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":0.9878000020980835,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9873999953269958,"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/algorithm","display_name":"Algorithm","score":0.6078429818153381},{"id":"https://openalex.org/keywords/closure","display_name":"Closure (psychology)","score":0.5831551551818848},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.5317866802215576},{"id":"https://openalex.org/keywords/energy","display_name":"Energy (signal processing)","score":0.5130497217178345},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5050213932991028},{"id":"https://openalex.org/keywords/reliability","display_name":"Reliability (semiconductor)","score":0.4854791462421417},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4625757038593292},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.31166213750839233},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.2426769733428955},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.17958396673202515},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10790190100669861}],"concepts":[{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6078429818153381},{"id":"https://openalex.org/C146834321","wikidata":"https://www.wikidata.org/wiki/Q2979672","display_name":"Closure (psychology)","level":2,"score":0.5831551551818848},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.5317866802215576},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.5130497217178345},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5050213932991028},{"id":"https://openalex.org/C43214815","wikidata":"https://www.wikidata.org/wiki/Q7310987","display_name":"Reliability (semiconductor)","level":3,"score":0.4854791462421417},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4625757038593292},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.31166213750839233},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2426769733428955},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.17958396673202515},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10790190100669861},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C34447519","wikidata":"https://www.wikidata.org/wiki/Q179522","display_name":"Market economy","level":1,"score":0.0},{"id":"https://openalex.org/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.0},{"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/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"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":"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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019277","descriptor_name":"Entropy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.2c01076","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.2c01076","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:36583975","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36583975","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":0.8199999928474426,"display_name":"Affordable and clean energy"}],"awards":[{"id":"https://openalex.org/G2421122440","display_name":null,"funder_award_id":"82273856","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3876180389","display_name":null,"funder_award_id":"202102021151","funder_id":"https://openalex.org/F4320316875","funder_display_name":"Natural Science Foundation of Guangzhou City"},{"id":"https://openalex.org/G4135978206","display_name":null,"funder_award_id":"U1811462","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4406902704","display_name":null,"funder_award_id":"81903542","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7874789835","display_name":null,"funder_award_id":"2021YFB0300101","funder_id":"https://openalex.org/F4320321540","funder_display_name":"Ministry of Science and Technology of the People's Republic of China"}],"funders":[{"id":"https://openalex.org/F4320316875","display_name":"Natural Science Foundation of Guangzhou City","ror":null},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321540","display_name":"Ministry of Science and Technology of the People's Republic of China","ror":"https://ror.org/027s68j25"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1573009101","https://openalex.org/W1976499671","https://openalex.org/W1983450159","https://openalex.org/W1984481443","https://openalex.org/W1997125900","https://openalex.org/W2019962781","https://openalex.org/W2035078255","https://openalex.org/W2041902442","https://openalex.org/W2059832777","https://openalex.org/W2067174909","https://openalex.org/W2093327248","https://openalex.org/W2094890323","https://openalex.org/W2096264060","https://openalex.org/W2106140689","https://openalex.org/W2137608611","https://openalex.org/W2140151763","https://openalex.org/W2154670681","https://openalex.org/W2166550586","https://openalex.org/W2308220327","https://openalex.org/W2323942455","https://openalex.org/W2404280981","https://openalex.org/W2558870009","https://openalex.org/W2607560340","https://openalex.org/W2738737407","https://openalex.org/W2772606519","https://openalex.org/W2794694420","https://openalex.org/W2807109642","https://openalex.org/W2891791233","https://openalex.org/W2914266147","https://openalex.org/W2917351232","https://openalex.org/W2954094311","https://openalex.org/W3008905875","https://openalex.org/W3047663514","https://openalex.org/W3090513030","https://openalex.org/W3092297806","https://openalex.org/W3111206976","https://openalex.org/W3216218913"],"related_works":["https://openalex.org/W315394019","https://openalex.org/W2923398117","https://openalex.org/W4309585848","https://openalex.org/W2265383332","https://openalex.org/W4328130279","https://openalex.org/W2002342158","https://openalex.org/W2105009749","https://openalex.org/W4299387245","https://openalex.org/W583262921","https://openalex.org/W1609156475"],"abstract_inverted_index":{"Free":[0],"energy":[1,5],"perturbation-relative":[2],"binding":[3,19],"free":[4],"(FEP-RBFE)":[6],"prediction":[7,16],"has":[8,49],"shown":[9],"its":[10],"reliability":[11],"and":[12,45,106,155,182],"accuracy":[13,60,115],"in":[14,26,56,83,104,136,205],"the":[15,33,58,63,73,84,90,109,113,130,162,185,214,218],"of":[17,35,66,68,112,217],"protein-ligand":[18],"affinities,":[20],"which":[21,98,173,200],"plays":[22],"a":[23,42,78,125,142,169,193],"fundamental":[24],"role":[25],"structure-based":[27],"drug":[28],"design.":[29],"In":[30,139],"FEP-RBFE":[31],"predictions,":[32],"calculation":[34,59,114,186,198],"each":[36,69],"mutation":[37],"path":[38],"is":[39,92,99],"associated":[40],"with":[41,213],"statistical":[43],"error,":[44],"cycle":[46,71,86,132,149],"closure":[47,87,133,150],"(cc)":[48],"proven":[50],"to":[51,72,95,101],"be":[52,102,202],"an":[53],"effective":[54],"method":[55,88,134,165,172,216],"improving":[57],"by":[61],"correcting":[62],"hysteresis":[64,91],"(summation":[65],"errors)":[67],"closed":[70,126],"theoretical":[74],"value":[75],"0.":[76],"However,":[77],"primary":[79],"hypothesis":[80],"was":[81,153],"made":[82],"current":[85,131],"that":[89],"evenly":[93],"distributed":[94],"all":[96],"paths,":[97],"unlikely":[100],"true":[103],"practice":[105],"may":[107],"limit":[108],"further":[110,183],"improvement":[111],"when":[116],"better":[117],"error":[118,177,197],"estimation":[119],"methods":[120],"are":[121],"available.":[122],"Moreover,":[123],"being":[124],"source":[127,146],"software":[128],"makes":[129],"unachievable":[135],"many":[137,206],"studies.":[138],"this":[140],"paper,":[141],"newly":[143],"implemented":[144],"open":[145],"graph-based":[147],"weighted":[148],"(wcc)":[151],"algorithm":[152],"developed":[154],"introduced,":[156],"not":[157],"only":[158],"including":[159],"functions":[160],"from":[161,179],"original":[163,219],"cc":[164,220],"but":[166],"also":[167,191],"containing":[168],"new":[170,194],"wcc":[171,189],"can":[174,201],"consider":[175],"different":[176,180],"contributions":[178],"paths":[181],"improve":[184],"accuracy.":[187],"The":[188],"program":[190],"provides":[192],"path-independent":[195],"molecular":[196],"method,":[199],"quite":[203],"useful":[204],"studies":[207],"(like":[208],"structure-activity":[209],"relationship":[210],"(SAR))":[211],"compared":[212],"path-dependent":[215],"program.":[221]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
