{"id":"https://openalex.org/W4409738279","doi":"https://doi.org/10.1093/bib/bbaf190","title":"Shared-weight graph framework for comprehensive protein stability prediction across diverse mutation types","display_name":"Shared-weight graph framework for comprehensive protein stability prediction across diverse mutation types","publication_year":2025,"publication_date":"2025-03-01","ids":{"openalex":"https://openalex.org/W4409738279","doi":"https://doi.org/10.1093/bib/bbaf190","pmid":"https://pubmed.ncbi.nlm.nih.gov/40273428"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf190","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf190","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbaf190","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100357036","display_name":"Gen Li","orcid":"https://orcid.org/0000-0002-6862-5547"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gen Li","raw_affiliation_strings":["Production and R&D Center I of LSS, GenScript (Shanghai) Biotech Co., Ltd. , 186 He Dan Road, Pudong New Area, Shanghai 200131 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Production and R&D Center I of LSS, GenScript (Shanghai) Biotech Co., Ltd. , 186 He Dan Road, Pudong New Area, Shanghai 200131 ,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102600236","display_name":"Sijie Yao","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sijie Yao","raw_affiliation_strings":["Production and R&D Center I of LSS, GenScript (Shanghai) Biotech Co., Ltd. , 186 He Dan Road, Pudong New Area, Shanghai 200131 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Production and R&D Center I of LSS, GenScript (Shanghai) Biotech Co., Ltd. , 186 He Dan Road, Pudong New Area, Shanghai 200131 ,","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060417628","display_name":"Long Fan","orcid":"https://orcid.org/0000-0001-8938-2225"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Long Fan","raw_affiliation_strings":["Production and R&D Center I of LSS, GenScript (Shanghai) Biotech Co., Ltd. , 186 He Dan Road, Pudong New Area, Shanghai 200131 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Production and R&D Center I of LSS, GenScript (Shanghai) Biotech Co., Ltd. , 186 He Dan Road, Pudong New Area, Shanghai 200131 ,","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.4868,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.61855909,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"26","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9940999746322632,"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":0.9940999746322632,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","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/T10171","display_name":"Biofuel production and bioconversion","score":0.9842000007629395,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/indel","display_name":"Indel","score":0.7465634346008301},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6690018773078918},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.5701361894607544},{"id":"https://openalex.org/keywords/point-mutation","display_name":"Point mutation","score":0.4839973449707031},{"id":"https://openalex.org/keywords/indel-mutation","display_name":"INDEL Mutation","score":0.47287365794181824},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4600216746330261},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4360502064228058},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.4264923334121704},{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.4214378595352173},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3115759789943695},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2811274528503418},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24662548303604126},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.16793903708457947},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09539484977722168}],"concepts":[{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.7465634346008301},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6690018773078918},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5701361894607544},{"id":"https://openalex.org/C176944494","wikidata":"https://www.wikidata.org/wiki/Q1415380","display_name":"Point mutation","level":4,"score":0.4839973449707031},{"id":"https://openalex.org/C2910714999","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"INDEL Mutation","level":5,"score":0.47287365794181824},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4600216746330261},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4360502064228058},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.4264923334121704},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.4214378595352173},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3115759789943695},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2811274528503418},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24662548303604126},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.16793903708457947},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09539484977722168},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.0}],"mesh":[{"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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf190","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf190","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40273428","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40273428","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:10831236","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12021015","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf190","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf190","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8598277215","display_name":null,"funder_award_id":"24QB2703300","funder_id":"https://openalex.org/F4320327803","funder_display_name":"Shanghai Rising-Star Program"}],"funders":[{"id":"https://openalex.org/F4320327803","display_name":"Shanghai Rising-Star Program","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1501132333","https://openalex.org/W2016655842","https://openalex.org/W2022438793","https://openalex.org/W2023490488","https://openalex.org/W2024405748","https://openalex.org/W2031553026","https://openalex.org/W2041476324","https://openalex.org/W2047659421","https://openalex.org/W2048125591","https://openalex.org/W2050688103","https://openalex.org/W2067950795","https://openalex.org/W2102541127","https://openalex.org/W2147864921","https://openalex.org/W2153195964","https://openalex.org/W2155733474","https://openalex.org/W2469640117","https://openalex.org/W2524049272","https://openalex.org/W2607211030","https://openalex.org/W2951433247","https://openalex.org/W2953906682","https://openalex.org/W2956569764","https://openalex.org/W2980789587","https://openalex.org/W3045908771","https://openalex.org/W3080555959","https://openalex.org/W3083008290","https://openalex.org/W3119533938","https://openalex.org/W3123504295","https://openalex.org/W3157949392","https://openalex.org/W3164046276","https://openalex.org/W3177500196","https://openalex.org/W4206007286","https://openalex.org/W4210535996","https://openalex.org/W4211001953","https://openalex.org/W4220883530","https://openalex.org/W4229331784","https://openalex.org/W4283212141","https://openalex.org/W4327550249","https://openalex.org/W4367183963","https://openalex.org/W4384820649","https://openalex.org/W4389608298","https://openalex.org/W4390096709","https://openalex.org/W4390521376","https://openalex.org/W4391308485","https://openalex.org/W4391431979","https://openalex.org/W4399202629","https://openalex.org/W4400358823","https://openalex.org/W4400921915","https://openalex.org/W4408505021","https://openalex.org/W6644614504","https://openalex.org/W6763868836","https://openalex.org/W6781932242"],"related_works":["https://openalex.org/W1971376828","https://openalex.org/W2135846417","https://openalex.org/W2167094946","https://openalex.org/W3092864927","https://openalex.org/W4206406917","https://openalex.org/W2080028493","https://openalex.org/W2046457574","https://openalex.org/W3103976079","https://openalex.org/W4409340179","https://openalex.org/W2010589665"],"abstract_inverted_index":{"Research":[0],"on":[1,39,59,133],"protein":[2,102,147,172],"stability":[3,17,148],"changes":[4,25],"is":[5,51,151],"vital":[6],"for":[7,75,85],"understanding":[8],"disease":[9],"mechanisms":[10],"and":[11,31,44,81,105,127,167,176],"optimizing":[12],"industrial":[13],"enzymes.":[14],"Protein":[15],"thermal":[16],"can":[18],"be":[19],"modified":[20],"by":[21],"variants":[22],"leading":[23],"to":[24,53,69,109,156,171],"in":[26,145],"\u0394\u0394G":[27],"values":[28],"between":[29],"wild-type":[30],"mutant":[32],"proteins.":[33],"Despite":[34],"advances,":[35],"most":[36],"models":[37,104],"focus":[38],"single-point":[40,49],"mutations,":[41,140],"overlooking":[42],"multipoint":[43,76],"indel":[45,89],"mutations.":[46,90],"Typically,":[47],"the":[48,60,121,134],"mutation":[50,159],"expected":[52],"have":[54],"a":[55,63,97,152],"relatively":[56],"limited":[57],"impact":[58],"function":[61],"of":[62,88,113,123],"protein,":[64],"necessitating":[65],"more":[66],"drastic":[67],"modifications":[68],"meet":[70],"new":[71],"challenges.":[72],"Current":[73],"methods":[74,144],"mutations":[77],"yield":[78],"poor":[79],"results,":[80],"no":[82],"method":[83],"exists":[84],"any":[86,111],"length":[87],"To":[91],"address":[92],"this,":[93],"we":[94],"introduce":[95],"UniMutStab,":[96],"shared-graph":[98],"convolutional":[99],"network":[100],"leveraging":[101],"language":[103],"residue":[106,124],"interaction":[107],"networks":[108],"access":[110],"type":[112],"mutation.":[114],"An":[115],"embedded":[116],"edge":[117],"weight":[118],"module":[119],"enhances":[120],"integration":[122],"node":[125],"features":[126],"interactions,":[128],"improving":[129],"prediction":[130],"accuracy.":[131],"Trained":[132],"\"Mega-scale\"":[135],"dataset":[136],"with":[137],"~780":[138],"000":[139],"UniMutStab":[141],"surpasses":[142],"existing":[143],"predicting":[146],"changes.":[149],"It":[150],"purely":[153],"sequence-based":[154],"approach":[155],"predict":[157],"arbitrary":[158],"types,":[160],"demonstrating":[161],"robust":[162],"generalization":[163],"across":[164],"multiple":[165],"tasks":[166],"potentially":[168],"contributing":[169],"significantly":[170],"engineering,":[173],"personalized":[174],"therapeutics,":[175],"diagnostic":[177],"methodologies.":[178]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}