{"id":"https://openalex.org/W4406261053","doi":"https://doi.org/10.1109/bibm62325.2024.10821753","title":"MEMO-stab: Sequence-based Annotation of Mutation Effect on Transmembrane Protein Stability with Protein Language Model-Driven Machine Learning","display_name":"MEMO-stab: Sequence-based Annotation of Mutation Effect on Transmembrane Protein Stability with Protein Language Model-Driven Machine Learning","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406261053","doi":"https://doi.org/10.1109/bibm62325.2024.10821753"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10821753","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10821753","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5100462338","display_name":"Zhe Liu","orcid":"https://orcid.org/0000-0001-6753-0303"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I2802690428","display_name":"Shanghai Mental Health Center","ror":"https://ror.org/05bd2wa15","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2802690428"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhe Liu","raw_affiliation_strings":["Shanghai Jiao Tong University,Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine School of Biomedical Engineering,Shanghai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine School of Biomedical Engineering,Shanghai,China","institution_ids":["https://openalex.org/I2802690428","https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004423488","display_name":"Yihang Bao","orcid":"https://orcid.org/0000-0002-8431-3412"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I2802690428","display_name":"Shanghai Mental Health Center","ror":"https://ror.org/05bd2wa15","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2802690428"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yihang Bao","raw_affiliation_strings":["Shanghai Jiao Tong University,Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine School of Biomedical Engineering,Shanghai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine School of Biomedical Engineering,Shanghai,China","institution_ids":["https://openalex.org/I2802690428","https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100362616","display_name":"Wenhao Li","orcid":"https://orcid.org/0000-0001-9439-4781"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I2802690428","display_name":"Shanghai Mental Health Center","ror":"https://ror.org/05bd2wa15","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2802690428"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenhao Li","raw_affiliation_strings":["Shanghai Jiao Tong University,Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine School of Biomedical Engineering,Shanghai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine School of Biomedical Engineering,Shanghai,China","institution_ids":["https://openalex.org/I2802690428","https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101421242","display_name":"Weihao Li","orcid":"https://orcid.org/0000-0001-5829-3887"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I2802690428","display_name":"Shanghai Mental Health Center","ror":"https://ror.org/05bd2wa15","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2802690428"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weihao Li","raw_affiliation_strings":["Shanghai Jiao Tong University,Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine School of Biomedical Engineering,Shanghai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine School of Biomedical Engineering,Shanghai,China","institution_ids":["https://openalex.org/I2802690428","https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019386958","display_name":"Weidi Wang","orcid":"https://orcid.org/0000-0002-6312-0689"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I2802690428","display_name":"Shanghai Mental Health Center","ror":"https://ror.org/05bd2wa15","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2802690428"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weidi Wang","raw_affiliation_strings":["Shanghai Jiao Tong University,Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine School of Biomedical Engineering,Shanghai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine School of Biomedical Engineering,Shanghai,China","institution_ids":["https://openalex.org/I2802690428","https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047609717","display_name":"Guan Ning Lin","orcid":"https://orcid.org/0000-0001-9496-0149"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I2802690428","display_name":"Shanghai Mental Health Center","ror":"https://ror.org/05bd2wa15","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I2802690428"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guan Ning Lin","raw_affiliation_strings":["Shanghai Jiao Tong University,Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine School of Biomedical Engineering,Shanghai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine School of Biomedical Engineering,Shanghai,China","institution_ids":["https://openalex.org/I2802690428","https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.6123,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.69634959,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"62","last_page":"66"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.993399977684021,"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":0.993399977684021,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9610000252723694,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.955299973487854,"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/computer-science","display_name":"Computer science","score":0.6539802551269531},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6052010655403137},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6020629405975342},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.5332234501838684},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4827810823917389},{"id":"https://openalex.org/keywords/stab","display_name":"Stab","score":0.46556949615478516},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.4556260108947754},{"id":"https://openalex.org/keywords/transmembrane-protein","display_name":"Transmembrane protein","score":0.4419354796409607},{"id":"https://openalex.org/keywords/protein-stability","display_name":"Protein stability","score":0.43337953090667725},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3941424489021301},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3398408889770508},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.23269373178482056},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15478762984275818},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.1294565498828888},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12222659587860107},{"id":"https://openalex.org/keywords/anatomy","display_name":"Anatomy","score":0.08216521143913269}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6539802551269531},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6052010655403137},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6020629405975342},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5332234501838684},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4827810823917389},{"id":"https://openalex.org/C2777085867","wikidata":"https://www.wikidata.org/wiki/Q7595695","display_name":"Stab","level":2,"score":0.46556949615478516},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.4556260108947754},{"id":"https://openalex.org/C24530287","wikidata":"https://www.wikidata.org/wiki/Q424204","display_name":"Transmembrane protein","level":3,"score":0.4419354796409607},{"id":"https://openalex.org/C2988375501","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein stability","level":2,"score":0.43337953090667725},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3941424489021301},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3398408889770508},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.23269373178482056},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15478762984275818},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.1294565498828888},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12222659587860107},{"id":"https://openalex.org/C105702510","wikidata":"https://www.wikidata.org/wiki/Q514","display_name":"Anatomy","level":1,"score":0.08216521143913269},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10821753","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10821753","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309612","display_name":"Natural Science Foundation of Shanghai","ror":null},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322999","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W2008887848","https://openalex.org/W2020448616","https://openalex.org/W2023490488","https://openalex.org/W2064488723","https://openalex.org/W2132746917","https://openalex.org/W2136513422","https://openalex.org/W2149580316","https://openalex.org/W2153411138","https://openalex.org/W2295598076","https://openalex.org/W2403557561","https://openalex.org/W2515590865","https://openalex.org/W2767657273","https://openalex.org/W3028862763","https://openalex.org/W3086313594","https://openalex.org/W3180702046","https://openalex.org/W4300861364","https://openalex.org/W4327550249","https://openalex.org/W4381743315","https://openalex.org/W6763868836"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2288928943","https://openalex.org/W2358755282","https://openalex.org/W2619954689","https://openalex.org/W2625833328","https://openalex.org/W4405124681"],"abstract_inverted_index":{"Transmembrane":[0],"proteins":[1],"are":[2],"pivotal":[3],"drug":[4],"targets.":[5],"Accurately":[6],"predicting":[7],"the":[8,35,62,67,91,119,126],"impact":[9],"of":[10,21,40,64,69,79,94,121,134],"mutations":[11,65],"on":[12,30,43,66],"their":[13],"stability":[14,68],"can":[15],"serve":[16],"as":[17],"an":[18,74],"early":[19],"indicator":[20],"alterations":[22],"in":[23],"protein":[24,31,53,99],"function.":[25],"Existing":[26],"prediction":[27,131],"methods":[28],"based":[29],"crystal":[32],"structures":[33],"lack":[34],"capability":[36,93],"for":[37,138],"large-scale":[38],"annotation":[39],"mutation":[41,86,140],"effects":[42],"transmembrane":[44,70,129],"proteins.":[45,71],"In":[46],"this":[47],"study,":[48],"we":[49],"present":[50],"a":[51,85,104],"sequence-based":[52,128],"language":[54,100],"model-driven":[55],"machine":[56],"learning":[57],"framework,":[58],"MEMO-stab,":[59],"to":[60,116],"predict":[61],"effect":[63],"MEMO-stab":[72,95,124],"is":[73,87,125],"end-to-end":[75],"binary":[76],"classifier":[77],"capable":[78,133],"rapidly":[80],"and":[81,102],"extensively":[82],"annotating":[83],"whether":[84],"destabilizing.":[88],"We":[89,111],"evaluated":[90],"integrative":[92],"with":[96],"eight":[97],"diverse":[98],"models":[101],"conducted":[103],"performance":[105],"comparison":[106],"against":[107],"alternative":[108],"existing":[109],"methods.":[110,123],"also":[112],"designed":[113],"case":[114],"studies":[115],"further":[117],"illustrate":[118],"advantage":[120],"our":[122],"first":[127],"protein-specific":[130],"tool":[132],"achieving":[135],"reasonable":[136],"results":[137],"destabilizing":[139],"prediction.":[141]},"counts_by_year":[{"year":2025,"cited_by_count":3}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}