{"id":"https://openalex.org/W4406238237","doi":"https://doi.org/10.1109/bibm62325.2024.10822663","title":"Revolutionizing Enzyme Turnover Predictions with Non-Binary Reaction Fingerprints and AI","display_name":"Revolutionizing Enzyme Turnover Predictions with Non-Binary Reaction Fingerprints and AI","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406238237","doi":"https://doi.org/10.1109/bibm62325.2024.10822663"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822663","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822663","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":"conference-paper","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/A5015619506","display_name":"J. Cheng","orcid":null},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jibin Cheng","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100420548","display_name":"Cheng Chen","orcid":"https://orcid.org/0000-0002-4203-2145"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cheng Chen","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113115832","display_name":"Guishan Cui","orcid":null},"institutions":[{"id":"https://openalex.org/I1793135","display_name":"Yanbian University","ror":"https://ror.org/039xnh269","country_code":"CN","type":"education","lineage":["https://openalex.org/I1793135"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guishan Cui","raw_affiliation_strings":["Yanbian University,College of Geography and Ocean Sciences,Yanji,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yanbian University,College of Geography and Ocean Sciences,Yanji,China","institution_ids":["https://openalex.org/I1793135"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050266554","display_name":"Haitao Jiang","orcid":"https://orcid.org/0000-0001-5475-5183"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haitao Jiang","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074194686","display_name":"Xuefeng Cui","orcid":"https://orcid.org/0000-0003-0350-1495"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuefeng Cui","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.37533156,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"663","last_page":"668"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9927999973297119,"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":0.9927999973297119,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9769999980926514,"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":0.9711999893188477,"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/binary-number","display_name":"Binary number","score":0.6052566170692444},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.552509069442749},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18580633401870728},{"id":"https://openalex.org/keywords/arithmetic","display_name":"Arithmetic","score":0.0681474506855011}],"concepts":[{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.6052566170692444},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.552509069442749},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18580633401870728},{"id":"https://openalex.org/C94375191","wikidata":"https://www.wikidata.org/wiki/Q11205","display_name":"Arithmetic","level":1,"score":0.0681474506855011}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822663","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822663","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/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320337495","display_name":"Technology Development","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1498436455","https://openalex.org/W1508604947","https://openalex.org/W1976548998","https://openalex.org/W2116341502","https://openalex.org/W2124019798","https://openalex.org/W2157457604","https://openalex.org/W2170298003","https://openalex.org/W2618530766","https://openalex.org/W2743063996","https://openalex.org/W2766958291","https://openalex.org/W3010024687","https://openalex.org/W3123901912","https://openalex.org/W3136918052","https://openalex.org/W3146944767","https://openalex.org/W4224442792","https://openalex.org/W4226145240","https://openalex.org/W4283032119","https://openalex.org/W4299497354","https://openalex.org/W4313525580","https://openalex.org/W4313527263","https://openalex.org/W4327550249","https://openalex.org/W4384023735","https://openalex.org/W4388819402","https://openalex.org/W4392208003","https://openalex.org/W6755207826"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"The":[0],"turnover":[1,44],"number":[2],"(kcat)":[3],"is":[4,167],"a":[5,133],"crucial":[6,102],"measure":[7],"for":[8,160],"evaluating":[9],"enzyme":[10],"catalytic":[11],"efficiency,":[12],"significantly":[13],"influencing":[14],"studies":[15],"of":[16,46,163],"cellular":[17],"metabolism":[18],"and":[19,78,99,124,140],"resource":[20],"allocation.":[21],"Due":[22],"to":[23,41,59],"the":[24,43,83,87],"high":[25],"costs":[26],"associated":[27],"with":[28],"determining":[29],"kcat,":[30],"predictive":[31],"machine":[32],"learning":[33,135],"models":[34],"such":[35],"as":[36],"TurNuP":[37,153],"have":[38,67],"been":[39],"developed":[40,110],"predict":[42,158],"numbers":[45],"kinetically":[47],"uncharacterized":[48],"enzymes.":[49,165],"Existing":[50],"methods":[51],"rely":[52],"on":[53,138],"binary":[54,64],"Differential":[55],"Reaction":[56,112],"Fingerprints":[57,113],"(DRFPs)":[58],"represent":[60],"reactions.":[61],"However,":[62],"these":[63,107],"reaction":[65,103],"fingerprints":[66],"two":[68],"main":[69],"limitations.":[70],"First,":[71],"they":[72,92],"only":[73],"show":[74,150],"changes":[75],"between":[76,97],"substrates":[77,88,98],"products,":[79,100],"without":[80],"specifying":[81],"whether":[82],"change":[84],"occurs":[85],"in":[86,156],"or":[89],"products.":[90],"Second,":[91],"omit":[93],"information":[94],"about":[95],"similarities":[96],"missing":[101],"details.":[104],"To":[105],"overcome":[106],"issues,":[108],"we":[109],"Quaternary":[111],"(QRFPs)":[114],"by":[115,154],"incorporating":[116],"quaternary":[117],"structural":[118],"features.":[119],"Thus,":[120],"QRFPs":[121,139],"extend":[122],"DRFPs,":[123],"DRFPs":[125],"can":[126],"be":[127],"derived":[128],"from":[129],"QRFPs.":[130],"We":[131],"proposed":[132],"deep":[134],"method":[136],"based":[137],"pretrained":[141],"protein":[142],"language":[143],"model":[144],"ESM2,":[145],"called":[146],"TurNuP4.":[147],"Experimental":[148],"results":[149],"that":[151],"TurNuP4outperforms":[152],"18%":[155],"R2to":[157],"kcatvalues":[159],"natural":[161],"reactions":[162],"wild-type":[164],"Code":[166],"available":[168],"at":[169],"https://github.com/xfcui/TurNuP4.":[170]},"counts_by_year":[],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
