{"id":"https://openalex.org/W4408693799","doi":"https://doi.org/10.1186/s13321-025-00979-5","title":"An interpretable deep geometric learning model to predict the effects of mutations on protein\u2013protein interactions using large-scale protein language model","display_name":"An interpretable deep geometric learning model to predict the effects of mutations on protein\u2013protein interactions using large-scale protein language model","publication_year":2025,"publication_date":"2025-03-21","ids":{"openalex":"https://openalex.org/W4408693799","doi":"https://doi.org/10.1186/s13321-025-00979-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/40119464"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-00979-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00979-5","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00979-5","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00979-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071549343","display_name":"Caiya Zhang","orcid":"https://orcid.org/0000-0003-3773-4027"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Caiya Zhang","raw_affiliation_strings":["Department of Computer Science, Western University, London, ON, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Western University, London, ON, Canada","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006832624","display_name":"Yanzhi Sun","orcid":"https://orcid.org/0000-0002-3871-4047"},"institutions":[{"id":"https://openalex.org/I46247651","display_name":"University of Manitoba","ror":"https://ror.org/02gfys938","country_code":"CA","type":"education","lineage":["https://openalex.org/I46247651"]},{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Yan Sun","raw_affiliation_strings":["Department of Biochemistry, Western University, London, ON, Canada","Department of Computer Science, University of Manitoba, Winnipeg, MB, Canada","Department of Computer Science, Western University, London, ON, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Western University, London, ON, Canada","institution_ids":["https://openalex.org/I125749732"]},{"raw_affiliation_string":"Department of Computer Science, University of Manitoba, Winnipeg, MB, Canada","institution_ids":["https://openalex.org/I46247651"]},{"raw_affiliation_string":"Department of Computer Science, Western University, London, ON, Canada","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035024838","display_name":"Pingzhao Hu","orcid":"https://orcid.org/0000-0002-9546-2245"},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]},{"id":"https://openalex.org/I46247651","display_name":"University of Manitoba","ror":"https://ror.org/02gfys938","country_code":"CA","type":"education","lineage":["https://openalex.org/I46247651"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Pingzhao Hu","raw_affiliation_strings":["Department of Biochemistry, Western University, London, ON, Canada. phu49@uwo.ca","Department of Computer Science, University of Manitoba, Winnipeg, MB, Canada. phu49@uwo.ca","Department of Computer Science, Western University, London, ON, Canada. phu49@uwo.ca","Department of Epidemiology and Biostatistics, Western University, London, ON, Canada. phu49@uwo.ca","Department of Oncology, Western University, London, ON, Canada. phu49@uwo.ca","The Children's Health Research Institute, Lawson Health Research Institute, London, ON, Canada. phu49@uwo.ca","Department of Computer Science, Western University, London, ON, Canada","Department of Biochemistry, Western University, London, ON, Canada","Department of Computer Science, University of Manitoba, Winnipeg, MB, Canada"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, Western University, London, ON, Canada. phu49@uwo.ca","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, University of Manitoba, Winnipeg, MB, Canada. phu49@uwo.ca","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, Western University, London, ON, Canada. phu49@uwo.ca","institution_ids":[]},{"raw_affiliation_string":"Department of Epidemiology and Biostatistics, Western University, London, ON, Canada. phu49@uwo.ca","institution_ids":[]},{"raw_affiliation_string":"Department of Oncology, Western University, London, ON, Canada. phu49@uwo.ca","institution_ids":[]},{"raw_affiliation_string":"The Children's Health Research Institute, Lawson Health Research Institute, London, ON, Canada. phu49@uwo.ca","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, Western University, London, ON, Canada","institution_ids":["https://openalex.org/I125749732"]},{"raw_affiliation_string":"Department of Biochemistry, Western University, London, ON, Canada","institution_ids":["https://openalex.org/I125749732"]},{"raw_affiliation_string":"Department of Computer Science, University of Manitoba, Winnipeg, MB, Canada","institution_ids":["https://openalex.org/I46247651"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5071549343"],"corresponding_institution_ids":["https://openalex.org/I125749732"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":2.8975,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.89947115,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"17","issue":"1","first_page":"35","last_page":"35"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9973000288009644,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9973000288009644,"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":0.9929999709129333,"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":0.9918000102043152,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6248646378517151},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.5688937306404114},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.47126126289367676},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3984265625476837}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6248646378517151},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5688937306404114},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.47126126289367676},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3984265625476837},{"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/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13321-025-00979-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00979-5","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00979-5","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:40119464","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40119464","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 cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:c64b31e652c34e36a7e1abad95f571d1","is_oa":true,"landing_page_url":"https://doaj.org/article/c64b31e652c34e36a7e1abad95f571d1","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 17, Iss 1, Pp 1-13 (2025)","raw_type":"article"},{"id":"pmh:oai:mspace.lib.umanitoba.ca:1993/39011","is_oa":false,"landing_page_url":"http://hdl.handle.net/1993/39011","pdf_url":null,"source":{"id":"https://openalex.org/S4306400554","display_name":"Mspace (University of Manitoba)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I46247651","host_organization_name":"University of Manitoba","host_organization_lineage":["https://openalex.org/I46247651"],"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":"research article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11927297","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11927297","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-00979-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00979-5","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00979-5","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1539477904","display_name":null,"funder_award_id":"PLL 185683","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G190741868","display_name":null,"funder_award_id":"RGPIN-2021-04072","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"},{"id":"https://openalex.org/G2157070843","display_name":null,"funder_award_id":"PJT 190272","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"},{"id":"https://openalex.org/G8374923726","display_name":null,"funder_award_id":"CRC-2021-00482","funder_id":"https://openalex.org/F4320334506","funder_display_name":"Canadian Institutes of Health Research"}],"funders":[{"id":"https://openalex.org/F4320334506","display_name":"Canadian Institutes of Health Research","ror":"https://ror.org/01gavpb45"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4408693799.pdf"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1222201926","https://openalex.org/W2036990405","https://openalex.org/W2112702439","https://openalex.org/W2136513422","https://openalex.org/W2172034373","https://openalex.org/W2201713963","https://openalex.org/W2618265628","https://openalex.org/W2907492528","https://openalex.org/W2909255640","https://openalex.org/W2944245644","https://openalex.org/W2945403072","https://openalex.org/W2953103783","https://openalex.org/W2969996838","https://openalex.org/W2995387264","https://openalex.org/W2996378307","https://openalex.org/W2999044305","https://openalex.org/W3005822506","https://openalex.org/W3007500173","https://openalex.org/W3045012301","https://openalex.org/W3045100294","https://openalex.org/W3082498841","https://openalex.org/W3092403777","https://openalex.org/W3146944767","https://openalex.org/W3179934025","https://openalex.org/W3208696217","https://openalex.org/W4210257598","https://openalex.org/W4229031603","https://openalex.org/W4283310603","https://openalex.org/W4318071656","https://openalex.org/W4366823175","https://openalex.org/W4380989429","https://openalex.org/W4382246105","https://openalex.org/W6600175266"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"Protein-protein":[0],"interactions":[1,101,277,354],"(PPIs)":[2,355],"are":[3],"central":[4],"to":[5,33,52,81,121,194,197,258,271,316,324,331,349,417],"the":[6,59,68,88,100,125,129,142,150,164,183,199,254,339,369,377,401],"mechanisms":[7],"of":[8,70,84,124,132,149,158,167,211,218,301,341,372,403],"signaling":[9],"pathways":[10],"and":[11,29,63,139,181,213,227,240,253,282,285,312,364,375,420],"immune":[12,310],"responses,":[13],"which":[14],"can":[15,304,414],"help":[16],"us":[17],"understand":[18],"disease":[19,313,405],"etiology.":[20],"Therefore,":[21],"there":[22,41],"is":[23,192],"a":[24,44,116,145,172,206,214,265,342],"significant":[25,45],"need":[26],"for":[27,78,308,400],"efficient":[28],"rapid":[30],"automated":[31],"approaches":[32],"predict":[34,53,198,273,350],"changes":[35,54,201,274,351],"in":[36,47,55,202,275,338,352],"PPIs.":[37],"In":[38,110],"recent":[39],"years,":[40],"has":[42,75],"been":[43],"increase":[46],"applying":[48],"deep":[49],"learning":[50],"techniques":[51],"binding":[56,159,203],"affinity":[57,160,204],"between":[58],"original":[60],"protein":[61,168,175,185,288,317,383,409,424],"complex":[62,404],"its":[64],"mutant":[65,126,239,242],"variants.":[66],"Particularly,":[67],"adoption":[69],"graph":[71,118,267,345],"neural":[72,119,268,346],"networks":[73],"(GNNs)":[74],"gained":[76],"prominence":[77],"their":[79],"ability":[80],"learn":[82],"representations":[83,379],"protein-protein":[85,133,276,353,373],"complexes.":[86,134],"However,":[87],"conventional":[89],"GNNs":[90],"have":[91,114],"mainly":[92],"concentrated":[93],"on":[94,225,232],"capturing":[95],"local":[96,138,281,363],"features,":[97,141,169],"often":[98],"disregarding":[99],"among":[102],"distant":[103],"elements":[104],"that":[105,245],"hold":[106],"potential":[107],"important":[108],"information.":[109],"this":[111,302,320],"study,":[112],"we":[113,170],"developed":[115],"transformer-based":[117,266,344],"network":[120,269,347],"extract":[122],"features":[123,284,366],"segment":[127],"from":[128,368],"three-dimensional":[130,370],"structure":[131,371],"By":[135,279,359],"embracing":[136],"both":[137,237,362],"global":[140,184,283,365],"approach":[143,180,270,321,387],"ensures":[144],"more":[146,155],"comprehensive":[147,259],"understanding":[148,402],"intricate":[151],"relationships,":[152],"thus":[153],"promising":[154],"accurate":[156],"predictions":[157],"changes.":[161],"To":[162],"enhance":[163],"representation":[165],"capability":[166],"incorporate":[171],"large-scale":[173],"pre-trained":[174],"language":[176,289,384],"model":[177,191,247,292],"into":[178],"our":[179,246,291,386],"employ":[182],"feature":[186],"it":[187],"provides.":[188],"The":[189,299,411],"proposed":[190],"shown":[193],"be":[195,415],"able":[196],"mutation":[200],"with":[205,356,408],"root":[207],"mean":[208],"square":[209],"error":[210],"1.10":[212],"Pearson":[215],"correlation":[216],"coefficient":[217],"near":[219],"0.71,":[220],"as":[221],"demonstrated":[222],"by":[223,381],"performance":[224],"test":[226],"validation":[228],"cases.":[229],"Our":[230,262,334,394],"experiments":[231],"all":[233],"five":[234],"datasets,":[235],"including":[236],"single":[238],"multiple":[241],"cases,":[243],"demonstrate":[244],"outperforms":[248,293],"four":[249],"state-of-the-art":[250,294],"baseline":[251],"methods,":[252],"efficacy":[255],"was":[256],"subjected":[257],"experimental":[260],"evaluation.":[261],"study":[263,303],"introduces":[264],"accurately":[272],"(PPIs).":[278],"integrating":[280,361],"leveraging":[286,376],"pretrained":[287,382],"models,":[290,385],"methods":[295,390],"across":[296,391],"diverse":[297,392],"datasets.":[298,393],"results":[300],"provide":[305],"new":[306],"views":[307],"studying":[309],"responses":[311],"etiology":[314,406],"related":[315,330],"mutations.":[318,410,425],"Furthermore,":[319],"may":[322,396],"contribute":[323],"other":[325],"biological":[326,419],"or":[327],"biochemical":[328,421],"studies":[329],"PPIs.Scientific":[332],"contribution":[333,336],"scientific":[335],"lies":[337],"development":[340],"novel":[343,398,412],"tailored":[348],"excellent":[357],"accuracy.":[358],"seamlessly":[360],"extracted":[367],"complexes,":[374],"rich":[378],"provided":[380],"surpasses":[388],"existing":[389],"findings":[395],"offer":[397],"insights":[399],"associated":[407],"tool":[413],"applicable":[416],"various":[418],"investigations":[422],"involving":[423]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
