{"id":"https://openalex.org/W4414603337","doi":"https://doi.org/10.1109/access.2025.3615796","title":"Predictive Modeling of Multi-Label Enzyme Substrate using Machine Learning","display_name":"Predictive Modeling of Multi-Label Enzyme Substrate using Machine Learning","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4414603337","doi":"https://doi.org/10.1109/access.2025.3615796"},"language":"en","primary_location":{"id":"doi:10.1109/access.2025.3615796","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3615796","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1109/access.2025.3615796","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062453491","display_name":"Sana Tariq","orcid":"https://orcid.org/0000-0001-7437-5794"},"institutions":[{"id":"https://openalex.org/I194348271","display_name":"Government College University, Faisalabad","ror":"https://ror.org/051zgra59","country_code":"PK","type":"education","lineage":["https://openalex.org/I194348271"]}],"countries":["PK"],"is_corresponding":true,"raw_author_name":"Sana Tariq","raw_affiliation_strings":["Department of Computer Science, Government College University, Faisalabad, Pakistan"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Government College University, Faisalabad, Pakistan","institution_ids":["https://openalex.org/I194348271"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047173698","display_name":"Muhammad Umer Sarwar","orcid":"https://orcid.org/0000-0001-6790-1979"},"institutions":[{"id":"https://openalex.org/I194348271","display_name":"Government College University, Faisalabad","ror":"https://ror.org/051zgra59","country_code":"PK","type":"education","lineage":["https://openalex.org/I194348271"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Muhammad Umer Sarwar","raw_affiliation_strings":["Department of Computer Science, Government College University, Faisalabad, Pakistan"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Government College University, Faisalabad, Pakistan","institution_ids":["https://openalex.org/I194348271"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082204963","display_name":"Muhammad Kashif Hanif","orcid":"https://orcid.org/0000-0001-5150-2228"},"institutions":[{"id":"https://openalex.org/I194348271","display_name":"Government College University, Faisalabad","ror":"https://ror.org/051zgra59","country_code":"PK","type":"education","lineage":["https://openalex.org/I194348271"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Muhammad Kashif Hanif","raw_affiliation_strings":["Department of Computer Science, Government College University, Faisalabad, Pakistan"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Government College University, Faisalabad, Pakistan","institution_ids":["https://openalex.org/I194348271"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072217554","display_name":"Muhammad Irfan Khan","orcid":"https://orcid.org/0000-0003-1128-7337"},"institutions":[{"id":"https://openalex.org/I194348271","display_name":"Government College University, Faisalabad","ror":"https://ror.org/051zgra59","country_code":"PK","type":"education","lineage":["https://openalex.org/I194348271"]}],"countries":["PK"],"is_corresponding":false,"raw_author_name":"Muhammad Irfan Khan","raw_affiliation_strings":["Department of Computer Science, Government College University, Faisalabad, Pakistan"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Government College University, Faisalabad, Pakistan","institution_ids":["https://openalex.org/I194348271"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5062453491"],"corresponding_institution_ids":["https://openalex.org/I194348271"],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.29212006,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9510999917984009,"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":0.9510999917984009,"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/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9325000047683716,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11124","display_name":"Protein purification and stability","score":0.9199000000953674,"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/benchmark","display_name":"Benchmark (surveying)","score":0.7056000232696533},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.5483999848365784},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.45210000872612},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.42160001397132874},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.36959999799728394},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.36079999804496765},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.3325999975204468},{"id":"https://openalex.org/keywords/predictive-modelling","display_name":"Predictive modelling","score":0.3301999866962433}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7613999843597412},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7350000143051147},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7056000232696533},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.7028999924659729},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.5483999848365784},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.45210000872612},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.42160001397132874},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.36959999799728394},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.36079999804496765},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3328999876976013},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3325999975204468},{"id":"https://openalex.org/C45804977","wikidata":"https://www.wikidata.org/wiki/Q7239673","display_name":"Predictive modelling","level":2,"score":0.3301999866962433},{"id":"https://openalex.org/C2777289219","wikidata":"https://www.wikidata.org/wiki/Q7632154","display_name":"Substrate (aquarium)","level":2,"score":0.3174999952316284},{"id":"https://openalex.org/C2994592520","wikidata":"https://www.wikidata.org/wiki/Q5090496","display_name":"Substrate specificity","level":3,"score":0.2930000126361847},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.29019999504089355},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.28999999165534973},{"id":"https://openalex.org/C2776482837","wikidata":"https://www.wikidata.org/wiki/Q3553958","display_name":"Multi-label classification","level":2,"score":0.2856999933719635},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.271699994802475},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.2703999876976013},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.2671000063419342},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.26429998874664307},{"id":"https://openalex.org/C2779715943","wikidata":"https://www.wikidata.org/wiki/Q427492","display_name":"Enzyme inhibition","level":3,"score":0.25110000371932983}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/access.2025.3615796","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3615796","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:2809d612631c460ba56f62b1be280fe4","is_oa":true,"landing_page_url":"https://doaj.org/article/2809d612631c460ba56f62b1be280fe4","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":"IEEE Access, Vol 13, Pp 172657-172673 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2025.3615796","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3615796","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Enzymes":[0],"play":[1],"a":[2,68,97,164],"critical":[3],"role":[4],"in":[5,19,140,183,192],"catalyzing":[6],"biochemical":[7],"reactions,":[8],"and":[9,24,32,60,92,126],"accurately":[10],"predicting":[11,41,141],"their":[12,61],"substrate":[13,50],"specificity":[14],"is":[15],"essential":[16],"for":[17,49,73,143,189],"applications":[18],"drug":[20],"discovery,":[21],"metabolic":[22],"engineering,":[23],"biotechnology.":[25],"However,":[26],"traditional":[27],"experimental":[28],"methods":[29],"are":[30],"time-consuming":[31],"resource-intensive,":[33],"while":[34],"existing":[35],"computational":[36,193],"approaches":[37],"often":[38],"rely":[39],"on":[40,107,130],"Enzyme":[42],"Commission":[43],"(EC)":[44],"numbers":[45],"as":[46],"coarse":[47],"proxies":[48],"specificity,":[51],"failing":[52],"to":[53,155,178],"capture":[54],"the":[55,131,148,187],"many-to-many":[56],"relationships":[57],"between":[58],"enzymes":[59,145],"substrates.":[62],"In":[63],"this":[64],"study,":[65],"we":[66],"present":[67],"hybrid":[69,160],"deep":[70],"learning":[71],"framework":[72],"prediction":[74,157],"of":[75,124,128,147],"enzyme-substrate":[76],"interactions.":[77],"The":[78,110,135,159,172],"proposed":[79,115,173],"model":[80,85,136],"integrates":[81],"ProtT5":[82],"protein":[83],"language":[84],"embeddings":[86],"with":[87,120],"extended":[88,177],"connectivity":[89],"fingerprints":[90],"(ECFP4)":[91],"3D":[93],"molecular":[94],"descriptors":[95],"through":[96],"dedicated":[98],"geometric":[99],"attention":[100,161],"mechanism":[101,162],"that":[102,114],"dynamically":[103],"weights":[104],"features":[105],"based":[106],"interaction":[108],"patterns.":[109],"key":[111],"findings":[112],"demonstrate":[113],"approach":[116],"achieves":[117],"state-of-the-art":[118],"performance,":[119],"an":[121],"overall":[122],"accuracy":[123],"88.2%":[125],"F1-score":[127],"0.823":[129],"BRENDA":[132],"benchmark":[133],"dataset.":[134],"shows":[137],"particular":[138],"strength":[139],"interactions":[142],"promiscuous":[144],"(18.7%":[146],"dataset),":[149],"improving":[150],"recall":[151],"by":[152],"22%":[153],"compared":[154],"EC-based":[156],"methods.":[158],"provides":[163],"9.2%":[165],"AUC":[166],"improvement":[167],"over":[168],"static":[169],"feature":[170],"concatenation.":[171],"methodology":[174],"can":[175],"be":[176],"other":[179],"multi-label":[180],"classification":[181],"problems":[182],"biological":[184],"systems,":[185],"paving":[186],"way":[188],"future":[190],"advancements":[191],"biology.":[194]},"counts_by_year":[],"updated_date":"2026-03-07T16:01:11.037858","created_date":"2025-10-10T00:00:00"}
