{"id":"https://openalex.org/W4409738286","doi":"https://doi.org/10.1093/bib/bbaf187","title":"DEKP: a deep learning model for enzyme kinetic parameter prediction based on pretrained models and graph neural networks","display_name":"DEKP: a deep learning model for enzyme kinetic parameter prediction based on pretrained models and graph neural networks","publication_year":2025,"publication_date":"2025-03-01","ids":{"openalex":"https://openalex.org/W4409738286","doi":"https://doi.org/10.1093/bib/bbaf187","pmid":"https://pubmed.ncbi.nlm.nih.gov/40273427"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf187","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf187","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/bbaf187","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Yizhen Wang","orcid":"https://orcid.org/0000-0003-1049-3067"},"institutions":[{"id":"https://openalex.org/I75900474","display_name":"Hubei University","ror":"https://ror.org/03a60m280","country_code":"CN","type":"education","lineage":["https://openalex.org/I75900474"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yizhen Wang","raw_affiliation_strings":["School of Computer Science , Hubei University, No. 368 Youyi Road, 430062 Wuhan,"],"raw_orcid":"https://orcid.org/0000-0003-1049-3067","affiliations":[{"raw_affiliation_string":"School of Computer Science , Hubei University, No. 368 Youyi Road, 430062 Wuhan,","institution_ids":["https://openalex.org/I75900474"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103987806","display_name":"Li Cheng","orcid":"https://orcid.org/0000-0002-2012-3505"},"institutions":[{"id":"https://openalex.org/I75900474","display_name":"Hubei University","ror":"https://ror.org/03a60m280","country_code":"CN","type":"education","lineage":["https://openalex.org/I75900474"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li Cheng","raw_affiliation_strings":["Hubei Key Laboratory of Big Data Intelligent Analysis and Application , Hubei University, No. 368 Youyi Road, 430062 Wuhan,","Key Laboratory of Intelligent Sensing System and Security , Hubei University, Ministry of Education, No. 368 Youyi Road, 430062 Wuhan,","School of Computer Science , Hubei University, No. 368 Youyi Road, 430062 Wuhan,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hubei Key Laboratory of Big Data Intelligent Analysis and Application , Hubei University, No. 368 Youyi Road, 430062 Wuhan,","institution_ids":["https://openalex.org/I75900474"]},{"raw_affiliation_string":"Key Laboratory of Intelligent Sensing System and Security , Hubei University, Ministry of Education, No. 368 Youyi Road, 430062 Wuhan,","institution_ids":["https://openalex.org/I75900474"]},{"raw_affiliation_string":"School of Computer Science , Hubei University, No. 368 Youyi Road, 430062 Wuhan,","institution_ids":["https://openalex.org/I75900474"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101474457","display_name":"Yanyun Zhang","orcid":"https://orcid.org/0000-0002-8990-8220"},"institutions":[{"id":"https://openalex.org/I75900474","display_name":"Hubei University","ror":"https://ror.org/03a60m280","country_code":"CN","type":"education","lineage":["https://openalex.org/I75900474"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanyun Zhang","raw_affiliation_strings":["Hubei Key Laboratory of Big Data Intelligent Analysis and Application , Hubei University, No. 368 Youyi Road, 430062 Wuhan,","Key Laboratory of Intelligent Sensing System and Security , Hubei University, Ministry of Education, No. 368 Youyi Road, 430062 Wuhan,","School of Computer Science , Hubei University, No. 368 Youyi Road, 430062 Wuhan,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hubei Key Laboratory of Big Data Intelligent Analysis and Application , Hubei University, No. 368 Youyi Road, 430062 Wuhan,","institution_ids":["https://openalex.org/I75900474"]},{"raw_affiliation_string":"Key Laboratory of Intelligent Sensing System and Security , Hubei University, Ministry of Education, No. 368 Youyi Road, 430062 Wuhan,","institution_ids":["https://openalex.org/I75900474"]},{"raw_affiliation_string":"School of Computer Science , Hubei University, No. 368 Youyi Road, 430062 Wuhan,","institution_ids":["https://openalex.org/I75900474"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101390715","display_name":"Yujia Cao","orcid":"https://orcid.org/0009-0001-8832-5859"},"institutions":[{"id":"https://openalex.org/I75900474","display_name":"Hubei University","ror":"https://ror.org/03a60m280","country_code":"CN","type":"education","lineage":["https://openalex.org/I75900474"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yujia Cao","raw_affiliation_strings":["School of Computer Science , Hubei University, No. 368 Youyi Road, 430062 Wuhan,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science , Hubei University, No. 368 Youyi Road, 430062 Wuhan,","institution_ids":["https://openalex.org/I75900474"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083023211","display_name":"Daniyal Alghazzawi","orcid":"https://orcid.org/0000-0002-5533-3203"},"institutions":[{"id":"https://openalex.org/I185163786","display_name":"King Abdulaziz University","ror":"https://ror.org/02ma4wv74","country_code":"SA","type":"education","lineage":["https://openalex.org/I185163786"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Daniyal Alghazzawi","raw_affiliation_strings":["Faculty of Computing and Information Technology (FCIT) , 3599 King Abdulaziz University (KAU), Unit 3600, Jeddah 22254-7653,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computing and Information Technology (FCIT) , 3599 King Abdulaziz University (KAU), Unit 3600, Jeddah 22254-7653,","institution_ids":["https://openalex.org/I185163786"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I75900474"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":6.4022,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.96835094,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"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":0.9980000257492065,"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":0.9980000257492065,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9950000047683716,"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":0.9945999979972839,"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":0.7251096963882446},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6582154035568237},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6287752389907837},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5655860304832458},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5607897043228149},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4743034839630127},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.44048312306404114},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.42393845319747925},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.10072025656700134}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7251096963882446},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6582154035568237},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6287752389907837},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5655860304832458},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5607897043228149},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4743034839630127},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.44048312306404114},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.42393845319747925},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.10072025656700134},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf187","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf187","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:40273427","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40273427","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:10831238","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12021017","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/bbaf187","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf187","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":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W2047849624","https://openalex.org/W2130479394","https://openalex.org/W2156125289","https://openalex.org/W2157177751","https://openalex.org/W2462439856","https://openalex.org/W2561960911","https://openalex.org/W2588247834","https://openalex.org/W2766958291","https://openalex.org/W2767044445","https://openalex.org/W2781939187","https://openalex.org/W2795248196","https://openalex.org/W2891398396","https://openalex.org/W2903357856","https://openalex.org/W2949223833","https://openalex.org/W2953321375","https://openalex.org/W2980789587","https://openalex.org/W3105895642","https://openalex.org/W3140314916","https://openalex.org/W3146944767","https://openalex.org/W3164046276","https://openalex.org/W3177500196","https://openalex.org/W3179485843","https://openalex.org/W3186179742","https://openalex.org/W3207760869","https://openalex.org/W3211150579","https://openalex.org/W3211394146","https://openalex.org/W3211795435","https://openalex.org/W4283032119","https://openalex.org/W4296032638","https://openalex.org/W4307468223","https://openalex.org/W4308019830","https://openalex.org/W4308195246","https://openalex.org/W4309506674","https://openalex.org/W4313485929","https://openalex.org/W4327550249","https://openalex.org/W4379600237","https://openalex.org/W4384023735","https://openalex.org/W4389546039","https://openalex.org/W4390678097","https://openalex.org/W4391544240","https://openalex.org/W4401135618","https://openalex.org/W4408812130","https://openalex.org/W4409154912","https://openalex.org/W4409247344","https://openalex.org/W4409247544","https://openalex.org/W6798272402","https://openalex.org/W6804049574"],"related_works":["https://openalex.org/W4375867731","https://openalex.org/W2611989081","https://openalex.org/W2731899572","https://openalex.org/W4230611425","https://openalex.org/W4294635752","https://openalex.org/W4304166257","https://openalex.org/W4383066092","https://openalex.org/W2375480909","https://openalex.org/W3215138031","https://openalex.org/W4380075502"],"abstract_inverted_index":{"The":[0],"prediction":[1,44],"of":[2,83,96,119,149],"enzyme":[3,39,75,126,137,151],"kinetic":[4,76,138],"parameters":[5],"is":[6,46,142],"crucial":[7],"for":[8,159],"screening":[9,152],"enzymes":[10],"with":[11],"high":[12],"catalytic":[13,122],"efficiency":[14,123],"and":[15,35,61,86,154],"desired":[16],"characteristics":[17],"to":[18,31,49,53,125,144],"catalyze":[19],"natural":[20],"or":[21],"non-natural":[22],"reactions.":[23],"Data-driven":[24],"machine":[25],"learning":[26,73],"models":[27,82,134],"have":[28],"been":[29],"explored":[30],"reduce":[32],"experimental":[33],"cost":[34],"speed":[36],"up":[37],"the":[38,43,54,106,147,150],"design":[40],"process.":[41],"However,":[42],"performance":[45,107,148],"still":[47],"subject":[48],"significant":[50],"limitations":[51],"due":[52,124],"variance":[55],"in":[56,121,135],"sequence":[57,111],"similarity":[58,112],"between":[59],"training":[60],"testing":[62],"datasets.":[63],"In":[64],"this":[65],"work,":[66],"we":[67],"introduce":[68],"DEKP,":[69],"an":[70],"integrated":[71],"deep":[72],"approach":[74,102],"parameter":[77],"prediction.":[78],"It":[79],"leverages":[80],"pretrained":[81],"protein":[84,97],"sequences":[85],"incorporates":[87],"enhanced":[88],"graph":[89],"neural":[90],"networks":[91],"that":[92,130],"provide":[93,155],"comprehensive":[94],"representation":[95],"structural":[98],"features.":[99],"This":[100,140],"novel":[101],"can":[103],"effectively":[104],"alleviate":[105],"degradation":[108],"caused":[109],"by":[110],"variation.":[113],"Moreover,":[114],"it":[115],"provides":[116],"sensitive":[117],"detection":[118],"changes":[120],"mutations.":[127],"Experiments":[128],"validate":[129],"DEKP":[131],"outperforms":[132],"existing":[133],"predicting":[136],"parameters.":[139],"work":[141],"expected":[143],"significantly":[145],"improve":[146],"process":[153],"a":[156],"robust":[157],"tool":[158],"enzyme-directed":[160],"evolution":[161],"research.":[162]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":6}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
