{"id":"https://openalex.org/W4408709554","doi":"https://doi.org/10.1109/tcbbio.2025.3552846","title":"SEFP: Structure-Based Enzyme Function Prediction","display_name":"SEFP: Structure-Based Enzyme Function Prediction","publication_year":2025,"publication_date":"2025-03-21","ids":{"openalex":"https://openalex.org/W4408709554","doi":"https://doi.org/10.1109/tcbbio.2025.3552846","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811372"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3552846","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3552846","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5100404381","display_name":"Ziqi Zhang","orcid":"https://orcid.org/0000-0001-9503-960X"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ziqi Zhang","raw_affiliation_strings":["School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","School of Artificial Intelligence and Computer Science, Wuxi, China"],"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Wuxi, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108667936","display_name":"Guan Yu Yu","orcid":null},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guanqing Yu","raw_affiliation_strings":["School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","School of Artificial Intelligence and Computer Science, Wuxi, China"],"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Wuxi, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042607110","display_name":"Zhaohong Deng","orcid":"https://orcid.org/0000-0002-0790-6492"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhaohong Deng","raw_affiliation_strings":["School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","School of Artificial Intelligence and Computer Science, Wuxi, China"],"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Wuxi, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056979248","display_name":"Chuping Luo","orcid":"https://orcid.org/0000-0002-3192-9889"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chenxi Luo","raw_affiliation_strings":["School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","School of Artificial Intelligence and Computer Science, Wuxi, China"],"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Wuxi, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103263843","display_name":"Cheng Cai","orcid":"https://orcid.org/0000-0003-3277-3537"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cheng Cai","raw_affiliation_strings":["School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","School of Artificial Intelligence and Computer Science, Wuxi, China"],"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Wuxi, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Wei Zhang","orcid":"https://orcid.org/0009-0003-5785-7363"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Zhang","raw_affiliation_strings":["School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","School of Artificial Intelligence and Computer Science, Wuxi, China"],"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Wuxi, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012481094","display_name":"Fuping Hu","orcid":"https://orcid.org/0000-0001-6285-8916"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fuping Hu","raw_affiliation_strings":["School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","School of Artificial Intelligence and Computer Science, Wuxi, China"],"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]},{"raw_affiliation_string":"School of Artificial Intelligence and Computer Science, Wuxi, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048680068","display_name":"Kup\u2010Sze Choi","orcid":"https://orcid.org/0000-0003-0836-7088"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kup-Sze Choi","raw_affiliation_strings":["HL7 Hong Kong Ltd., Hong Kong"],"affiliations":[{"raw_affiliation_string":"HL7 Hong Kong Ltd., Hong Kong","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089693750","display_name":"Zhisheng Wei","orcid":null},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhisheng Wei","raw_affiliation_strings":["School of Biotechnology, Jiangnan University, Wuxi, China"],"affiliations":[{"raw_affiliation_string":"School of Biotechnology, Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100710637","display_name":"Lei Wang","orcid":"https://orcid.org/0000-0002-5065-8447"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Wang","raw_affiliation_strings":["School of Biotechnology, Jiangnan University, Wuxi, China"],"affiliations":[{"raw_affiliation_string":"School of Biotechnology, Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100778242","display_name":"Jing Wu","orcid":"https://orcid.org/0000-0001-8861-766X"},"institutions":[{"id":"https://openalex.org/I111599522","display_name":"Jiangnan University","ror":"https://ror.org/04mkzax54","country_code":"CN","type":"education","lineage":["https://openalex.org/I111599522"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Wu","raw_affiliation_strings":["School of Biotechnology, Jiangnan University, Wuxi, China"],"affiliations":[{"raw_affiliation_string":"School of Biotechnology, Jiangnan University, Wuxi, China","institution_ids":["https://openalex.org/I111599522"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5100404381"],"corresponding_institution_ids":["https://openalex.org/I111599522"],"apc_list":null,"apc_paid":null,"fwci":0.767,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.69243585,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"22","issue":"3","first_page":"1211","last_page":"1221"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9901000261306763,"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":0.9901000261306763,"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":0.9715999960899353,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9373000264167786,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3823959231376648},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3257884383201599},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1854986846446991}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3823959231376648},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3257884383201599},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1854986846446991}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3552846","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3552846","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811372","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811372","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2278947543","display_name":null,"funder_award_id":"62176105","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2321438132","display_name":null,"funder_award_id":"202406790100","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":39,"referenced_works":["https://openalex.org/W1968416380","https://openalex.org/W1996392933","https://openalex.org/W2026666393","https://openalex.org/W2036198912","https://openalex.org/W2064675550","https://openalex.org/W2077251274","https://openalex.org/W2097606916","https://openalex.org/W2112796928","https://openalex.org/W2122111042","https://openalex.org/W2129368756","https://openalex.org/W2131366108","https://openalex.org/W2162260681","https://openalex.org/W2170441710","https://openalex.org/W2598525602","https://openalex.org/W2615066396","https://openalex.org/W2739455021","https://openalex.org/W2766352633","https://openalex.org/W2800788706","https://openalex.org/W2801106948","https://openalex.org/W2892210937","https://openalex.org/W2946146152","https://openalex.org/W2951793362","https://openalex.org/W2953321375","https://openalex.org/W2982425557","https://openalex.org/W3028039738","https://openalex.org/W3136918052","https://openalex.org/W3164046276","https://openalex.org/W3186179742","https://openalex.org/W3193965968","https://openalex.org/W4236358448","https://openalex.org/W4239510810","https://openalex.org/W4296032638","https://openalex.org/W4388464011","https://openalex.org/W4389076255","https://openalex.org/W4400762160","https://openalex.org/W6726873649","https://openalex.org/W6739778489","https://openalex.org/W6763422710","https://openalex.org/W6843241131"],"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":{"Traditional":[0],"biological":[1],"experimental":[2],"methods":[3,28],"to":[4,13,33,66,86,120,181],"determine":[5],"enzyme":[6,21,35,47,51,62,89,99,142,201],"properties":[7],"are":[8,29,179],"time-consuming":[9],"and":[10,31,104,117,157,199,208],"costly,":[11],"leading":[12],"an":[14,147,173],"increasing":[15],"interest":[16],"in":[17,206],"computational":[18,27,134,209],"models":[19],"for":[20,50,197],"function":[22,52,202],"prediction.":[23,53],"However,":[24],"the":[25,68,74,93,122,140,160,183,193],"existing":[26],"insufficient":[30],"inefficient":[32],"exploit":[34],"structure.":[36],"In":[37],"this":[38],"work,":[39],"we":[40],"introduce":[41],"SEFP,":[42],"a":[43,60,82,108],"novel":[44],"method":[45],"leveraging":[46],"point":[48,63,90,116],"clouds":[49],"The":[54],"structure":[55,143],"encoder":[56,97],"of":[57,71,149,175,185,195],"SEFP":[58,114,130,145,163,196],"uses":[59],"tailored":[61],"cloud":[64],"network":[65],"analyze":[67],"three-dimensional":[69],"arrangement":[70],"atoms":[72],"within":[73,188],"enzyme,":[75],"integrating":[76],"hierarchical":[77],"residue":[78,83,95,100,118],"global":[79],"features":[80,101,119],"through":[81],"feature":[84,96],"adapter":[85],"extract":[87],"detailed":[88],"features.":[91],"Additionally,":[92],"Bio-BCS":[94],"extracts":[98],"with":[102],"channel":[103],"spatial":[105],"weights":[106],"using":[107],"specially":[109],"designed":[110],"attention":[111],"mechanism.":[112],"Finally,":[113],"fuses":[115],"generate":[121],"final":[123],"prediction":[124],"results.":[125],"Comparative":[126],"evaluations":[127],"show":[128],"that":[129],"outperforms":[131],"various":[132],"recent":[133],"methods,":[135,155,171],"demonstrating":[136],"superior":[137],"performance.":[138],"On":[139,159],"RSCB":[141],"dataset,":[144,162],"achieves":[146],"f1-score":[148,174],"95.85,":[150],"outperforming":[151],"two":[152],"representative":[153],"structure-based":[154],"EnzyNet":[156],"DeepFri.":[158],"HECNet":[161],"maintains":[164],"its":[165],"superiority":[166],"over":[167],"all":[168],"comparison":[169],"sequence-based":[170],"yielding":[172],"94.29.":[176],"Ablation":[177],"studies":[178],"conducted":[180],"confirm":[182],"effectiveness":[184],"individual":[186],"modules":[187],"SEFP.":[189],"These":[190],"findings":[191],"underscore":[192],"potential":[194],"reliable":[198],"precise":[200],"prediction,":[203],"offering":[204],"advancements":[205],"bioinformatics":[207],"biology.":[210]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
