{"id":"https://openalex.org/W4408461854","doi":"https://doi.org/10.1021/acs.jcim.4c02309","title":"Join Persistent Homology (JPH)-Based Machine Learning for Metalloprotein\u2013Ligand Binding Affinity Prediction","display_name":"Join Persistent Homology (JPH)-Based Machine Learning for Metalloprotein\u2013Ligand Binding Affinity Prediction","publication_year":2025,"publication_date":"2025-03-13","ids":{"openalex":"https://openalex.org/W4408461854","doi":"https://doi.org/10.1021/acs.jcim.4c02309","pmid":"https://pubmed.ncbi.nlm.nih.gov/40082211"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c02309","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c02309","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/A5010398295","display_name":"Yaxing Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yaxing Wang","raw_affiliation_strings":["Nankai University","School of Mathematical Sciences"],"raw_orcid":"https://orcid.org/0009-0006-4528-2963","affiliations":[{"raw_affiliation_string":"Nankai University","institution_ids":["https://openalex.org/I205237279"]},{"raw_affiliation_string":"School of Mathematical Sciences","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100408571","display_name":"Xiang Liu","orcid":"https://orcid.org/0000-0001-6046-1405"},"institutions":[{"id":"https://openalex.org/I530967","display_name":"Toronto Metropolitan University","ror":"https://ror.org/05g13zd79","country_code":"CA","type":"education","lineage":["https://openalex.org/I530967"]},{"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":["CA","US"],"is_corresponding":false,"raw_author_name":"Xiang Liu","raw_affiliation_strings":["Department of Mathematics","Michigan State University"],"raw_orcid":"https://orcid.org/0000-0001-6046-1405","affiliations":[{"raw_affiliation_string":"Department of Mathematics","institution_ids":["https://openalex.org/I530967"]},{"raw_affiliation_string":"Michigan State University","institution_ids":["https://openalex.org/I87216513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100730687","display_name":"Yipeng Zhang","orcid":"https://orcid.org/0000-0003-0664-5101"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]},{"id":"https://openalex.org/I4210163295","display_name":"Division of Mathematical Sciences","ror":"https://ror.org/051fftw81","country_code":"US","type":"government","lineage":["https://openalex.org/I1311060795","https://openalex.org/I4210112577","https://openalex.org/I4210163295"]}],"countries":["SG","US"],"is_corresponding":false,"raw_author_name":"Yipeng Zhang","raw_affiliation_strings":["Division of Mathematical Sciences, School of Physical and Mathematical Sciences","Nanyang Technological University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Mathematical Sciences, School of Physical and Mathematical Sciences","institution_ids":["https://openalex.org/I4210163295"]},{"raw_affiliation_string":"Nanyang Technological University","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111896318","display_name":"Xiangjun Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangjun Wang","raw_affiliation_strings":["Nankai University","School of Mathematical Sciences"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nankai University","institution_ids":["https://openalex.org/I205237279"]},{"raw_affiliation_string":"School of Mathematical Sciences","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5084610901","display_name":"Kelin Xia","orcid":"https://orcid.org/0000-0003-4183-0943"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]},{"id":"https://openalex.org/I4210163295","display_name":"Division of Mathematical Sciences","ror":"https://ror.org/051fftw81","country_code":"US","type":"government","lineage":["https://openalex.org/I1311060795","https://openalex.org/I4210112577","https://openalex.org/I4210163295"]}],"countries":["SG","US"],"is_corresponding":true,"raw_author_name":"Kelin Xia","raw_affiliation_strings":["Division of Mathematical Sciences, School of Physical and Mathematical Sciences","Nanyang Technological University"],"raw_orcid":"https://orcid.org/0000-0003-4183-0943","affiliations":[{"raw_affiliation_string":"Division of Mathematical Sciences, School of Physical and Mathematical Sciences","institution_ids":["https://openalex.org/I4210163295"]},{"raw_affiliation_string":"Nanyang Technological University","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5084610901"],"corresponding_institution_ids":["https://openalex.org/I172675005","https://openalex.org/I4210163295"],"apc_list":null,"apc_paid":null,"fwci":6.1977,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.96487718,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"65","issue":"6","first_page":"2785","last_page":"2793"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9987999796867371,"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":0.9987999796867371,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9879999756813049,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.963100016117096,"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/metalloprotein","display_name":"Metalloprotein","score":0.721642255783081},{"id":"https://openalex.org/keywords/join","display_name":"Join (topology)","score":0.7034839987754822},{"id":"https://openalex.org/keywords/homology","display_name":"Homology (biology)","score":0.5375160574913025},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4695855975151062},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4459277093410492},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.4355371594429016},{"id":"https://openalex.org/keywords/signal-transducing-adaptor-protein","display_name":"Signal transducing adaptor protein","score":0.4227715730667114},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.36526429653167725},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32188618183135986},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2968869209289551},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2464878261089325},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.2030070424079895},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.15485289692878723},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.130003422498703},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.07458299398422241}],"concepts":[{"id":"https://openalex.org/C17165728","wikidata":"https://www.wikidata.org/wiki/Q423350","display_name":"Metalloprotein","level":3,"score":0.721642255783081},{"id":"https://openalex.org/C2776124973","wikidata":"https://www.wikidata.org/wiki/Q3183033","display_name":"Join (topology)","level":2,"score":0.7034839987754822},{"id":"https://openalex.org/C165525559","wikidata":"https://www.wikidata.org/wiki/Q224180","display_name":"Homology (biology)","level":3,"score":0.5375160574913025},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4695855975151062},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4459277093410492},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.4355371594429016},{"id":"https://openalex.org/C183786373","wikidata":"https://www.wikidata.org/wiki/Q5964993","display_name":"Signal transducing adaptor protein","level":3,"score":0.4227715730667114},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.36526429653167725},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32188618183135986},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2968869209289551},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2464878261089325},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.2030070424079895},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.15485289692878723},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.130003422498703},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.07458299398422241},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008667","descriptor_name":"Metalloproteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.4c02309","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c02309","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:40082211","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40082211","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:dr.ntu.edu.sg:10356/202644","is_oa":false,"landing_page_url":"https://hdl.handle.net/10356/202644","pdf_url":null,"source":{"id":"https://openalex.org/S4306402609","display_name":"DR-NTU (Nanyang Technological University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I172675005","host_organization_name":"Nanyang Technological University","host_organization_lineage":["https://openalex.org/I172675005"],"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":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G337908427","display_name":null,"funder_award_id":"MOE-T2EP20221-0003","funder_id":"https://openalex.org/F4320320751","funder_display_name":"Ministry of Education - Singapore"},{"id":"https://openalex.org/G440546595","display_name":null,"funder_award_id":"MOE-T2EP20120-0010","funder_id":"https://openalex.org/F4320320751","funder_display_name":"Ministry of Education - Singapore"},{"id":"https://openalex.org/G6516556480","display_name":null,"funder_award_id":"12271183","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G752670138","display_name":null,"funder_award_id":"RG16/23","funder_id":"https://openalex.org/F4320320751","funder_display_name":"Ministry of Education - Singapore"}],"funders":[{"id":"https://openalex.org/F4320320751","display_name":"Ministry of Education - Singapore","ror":"https://ror.org/01kcva023"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W587309057","https://openalex.org/W1526753291","https://openalex.org/W1602508341","https://openalex.org/W1681224145","https://openalex.org/W1960392612","https://openalex.org/W1972156862","https://openalex.org/W1974727083","https://openalex.org/W1988037271","https://openalex.org/W1993285168","https://openalex.org/W2016779984","https://openalex.org/W2058170418","https://openalex.org/W2064186839","https://openalex.org/W2066326360","https://openalex.org/W2084168858","https://openalex.org/W2088162362","https://openalex.org/W2172216479","https://openalex.org/W2221103459","https://openalex.org/W2304387544","https://openalex.org/W2313042065","https://openalex.org/W2511842418","https://openalex.org/W2610142609","https://openalex.org/W2733638363","https://openalex.org/W2767581071","https://openalex.org/W2773405722","https://openalex.org/W2801991413","https://openalex.org/W2963833291","https://openalex.org/W3001282080","https://openalex.org/W3021453944","https://openalex.org/W3034639384","https://openalex.org/W3122618795","https://openalex.org/W3138367350","https://openalex.org/W3140655290","https://openalex.org/W3157078379","https://openalex.org/W3158144848","https://openalex.org/W4200074081","https://openalex.org/W4223481922","https://openalex.org/W4233690291","https://openalex.org/W4243631322","https://openalex.org/W4251358505","https://openalex.org/W4293582230","https://openalex.org/W4320006268","https://openalex.org/W4388440117","https://openalex.org/W4390575960","https://openalex.org/W4394582099","https://openalex.org/W4402728246"],"related_works":["https://openalex.org/W4205996836","https://openalex.org/W2151692181","https://openalex.org/W4392498349","https://openalex.org/W2093960938","https://openalex.org/W4407788647","https://openalex.org/W3214148052","https://openalex.org/W4392216655","https://openalex.org/W2807741550","https://openalex.org/W794462722","https://openalex.org/W2029625042"],"abstract_inverted_index":{"With":[0],"the":[1,15,56,97,100,112,126,131,139,161,180,190,199],"crucial":[2],"role":[3],"of":[4,19,47,88,99,125,130,165,179,193,201],"metalloproteins":[5,24],"in":[6,44,198],"respiration,":[7],"oxidative":[8],"stress":[9],"protection,":[10],"photosynthesis,":[11],"and":[12,17,39,50,63,79,104,163,204],"drug":[13,48],"metabolism,":[14],"design":[16,49],"discovery":[18],"drugs":[20],"that":[21,172],"can":[22,119,176],"target":[23],"are":[25,136],"extremely":[26],"important.":[27],"Recently,":[28],"enormous":[29],"potential":[30,192],"has":[31,169],"been":[32,170],"shown":[33],"by":[34],"topological":[35,128],"data":[36],"analysis":[37],"(TDA)":[38],"TDA-based":[40],"machine":[41,65],"learning":[42,66],"models":[43,67],"various":[45],"steps":[46],"discovery.":[51],"Here,":[52],"we":[53,186],"propose,":[54],"for":[55,68,96,145,153,160],"first":[57],"time,":[58],"join":[59,98,195],"persistent":[60,77,81,196],"homology":[61,78,197],"(JPH)":[62],"JPH-based":[64,116],"metalloprotein-ligand":[69,146,154],"binding":[70,147],"affinity":[71,148],"prediction.":[72,149],"Mathematically,":[73],"dramatically":[74],"different":[75],"from":[76,156],"extended":[80],"homology,":[82],"our":[83,115,166,173,194],"JPH":[84,134],"employs":[85],"a":[86,93,105,121],"set":[87],"filtration":[89,95],"functions":[90],"to":[91],"generate":[92],"multistage":[94],"original":[101],"simplicial":[102,109],"complex":[103],"specially":[106],"designed":[107],"test":[108],"complex.":[110],"From":[111],"featurization":[113],"perspective,":[114],"molecular":[117,202],"descriptors":[118,135],"provide":[120],"more":[122],"comprehensive":[123],"characterization":[124,200],"intrinsic":[127],"information":[129],"data.":[132],"Our":[133],"combined":[137],"with":[138],"gradient":[140],"boosting":[141],"tree":[142],"(GBT)":[143],"model":[144,175],"The":[150],"benchmark":[151],"dataset":[152],"complexes":[155],"PDBbind-v2020":[157],"is":[158],"employed":[159],"validation":[162],"comparison":[164],"model.":[167],"It":[168],"found":[171],"JPH-GBT":[174],"outperform":[177],"all":[178],"existing":[181],"models,":[182],"as":[183,185],"far":[184],"know.":[187],"This":[188],"demonstrates":[189],"great":[191],"structures":[203],"functions.":[205]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5}],"updated_date":"2025-12-28T23:10:05.387466","created_date":"2025-10-10T00:00:00"}