{"id":"https://openalex.org/W4406033692","doi":"https://doi.org/10.1093/bib/bbae695","title":"ProteinF3S: boosting enzyme function prediction by fusing protein sequence, structure, and surface","display_name":"ProteinF3S: boosting enzyme function prediction by fusing protein sequence, structure, and surface","publication_year":2024,"publication_date":"2024-11-22","ids":{"openalex":"https://openalex.org/W4406033692","doi":"https://doi.org/10.1093/bib/bbae695","pmid":"https://pubmed.ncbi.nlm.nih.gov/39750023"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae695","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae695","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/bbae695","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011879942","display_name":"Mingzhi Yuan","orcid":"https://orcid.org/0000-0003-1322-7530"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingzhi Yuan","raw_affiliation_strings":["Digital Medical Research Center , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","Fudan University , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University , 131 Dong\u2019an Road, 200032 Shanghai ,"],"raw_orcid":"https://orcid.org/0000-0003-1322-7530","affiliations":[{"raw_affiliation_string":"Digital Medical Research Center , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":[]},{"raw_affiliation_string":"Fudan University , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089201296","display_name":"Ao Shen","orcid":"https://orcid.org/0009-0001-1937-6855"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ao Shen","raw_affiliation_strings":["Digital Medical Research Center , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","Fudan University , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University , 131 Dong\u2019an Road, 200032 Shanghai ,"],"raw_orcid":"https://orcid.org/0009-0001-1937-6855","affiliations":[{"raw_affiliation_string":"Digital Medical Research Center , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":[]},{"raw_affiliation_string":"Fudan University , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103062942","display_name":"Yingfan Ma","orcid":"https://orcid.org/0009-0004-7335-785X"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yingfan Ma","raw_affiliation_strings":["Digital Medical Research Center , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","Fudan University , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University , 131 Dong\u2019an Road, 200032 Shanghai ,"],"raw_orcid":"https://orcid.org/0009-0004-7335-785X","affiliations":[{"raw_affiliation_string":"Digital Medical Research Center , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":[]},{"raw_affiliation_string":"Fudan University , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100594305","display_name":"Jie Du","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Du","raw_affiliation_strings":["Digital Medical Research Center , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","Fudan University , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University , 131 Dong\u2019an Road, 200032 Shanghai ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Digital Medical Research Center , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":[]},{"raw_affiliation_string":"Fudan University , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040711084","display_name":"Bohan An","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bohan An","raw_affiliation_strings":["Digital Medical Research Center , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","Fudan University , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University , 131 Dong\u2019an Road, 200032 Shanghai ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Digital Medical Research Center , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":[]},{"raw_affiliation_string":"Fudan University , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029371371","display_name":"Manning Wang","orcid":"https://orcid.org/0000-0002-9255-3897"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Manning Wang","raw_affiliation_strings":["Digital Medical Research Center , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","Fudan University , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University , 131 Dong\u2019an Road, 200032 Shanghai ,"],"raw_orcid":"https://orcid.org/0000-0002-9255-3897","affiliations":[{"raw_affiliation_string":"Digital Medical Research Center , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":[]},{"raw_affiliation_string":"Fudan University , School of Basic Medical Sciences, , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai Key Laboratory of Medical Image Computing and Computer Assisted Intervention, Fudan University , 131 Dong\u2019an Road, 200032 Shanghai ,","institution_ids":["https://openalex.org/I24943067"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I24943067"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.7465,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.71675048,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"26","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9994000196456909,"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":0.9994000196456909,"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":0.9983999729156494,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9962000250816345,"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":0.6874873638153076},{"id":"https://openalex.org/keywords/boosting","display_name":"Boosting (machine learning)","score":0.659634530544281},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6258662939071655},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.5891472101211548},{"id":"https://openalex.org/keywords/fusion","display_name":"Fusion","score":0.5382120013237},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5052796006202698},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.43850740790367126},{"id":"https://openalex.org/keywords/fuse","display_name":"Fuse (electrical)","score":0.42893359065055847},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.394178181886673},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.37402254343032837},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09119075536727905},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08071509003639221}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6874873638153076},{"id":"https://openalex.org/C46686674","wikidata":"https://www.wikidata.org/wiki/Q466303","display_name":"Boosting (machine learning)","level":2,"score":0.659634530544281},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6258662939071655},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.5891472101211548},{"id":"https://openalex.org/C158525013","wikidata":"https://www.wikidata.org/wiki/Q2593739","display_name":"Fusion","level":2,"score":0.5382120013237},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5052796006202698},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.43850740790367126},{"id":"https://openalex.org/C141353440","wikidata":"https://www.wikidata.org/wiki/Q182221","display_name":"Fuse (electrical)","level":2,"score":0.42893359065055847},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.394178181886673},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.37402254343032837},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09119075536727905},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08071509003639221},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae695","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae695","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39750023","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39750023","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:pubmedcentral.nih.gov:11697223","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11697223","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11697223/pdf/bbae695.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae695","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae695","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3250757299","display_name":null,"funder_award_id":"23S41900400","funder_id":"https://openalex.org/F4320321885","funder_display_name":"Science and Technology Commission of Shanghai Municipality"},{"id":"https://openalex.org/G7754111381","display_name":null,"funder_award_id":"23S41900400","funder_id":"https://openalex.org/F4320336652","funder_display_name":"Science and Technology Innovation Plan Of Shanghai Science and Technology Commission"}],"funders":[{"id":"https://openalex.org/F4320321851","display_name":"Fudan University","ror":"https://ror.org/013q1eq08"},{"id":"https://openalex.org/F4320321885","display_name":"Science and Technology Commission of Shanghai Municipality","ror":"https://ror.org/03kt66j61"},{"id":"https://openalex.org/F4320336652","display_name":"Science and Technology Innovation Plan Of Shanghai Science and Technology Commission","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W2096344315","https://openalex.org/W2102461176","https://openalex.org/W2103972113","https://openalex.org/W2106141559","https://openalex.org/W2106383417","https://openalex.org/W2112937261","https://openalex.org/W2118526609","https://openalex.org/W2138479935","https://openalex.org/W2144658220","https://openalex.org/W2163151214","https://openalex.org/W2322077141","https://openalex.org/W2496053465","https://openalex.org/W2784883284","https://openalex.org/W2951433247","https://openalex.org/W2992752586","https://openalex.org/W3005407385","https://openalex.org/W3098365587","https://openalex.org/W3146944767","https://openalex.org/W3164046276","https://openalex.org/W3177828909","https://openalex.org/W3196609471","https://openalex.org/W4205773061","https://openalex.org/W4212863985","https://openalex.org/W4224939843","https://openalex.org/W4225726305","https://openalex.org/W4297733535","https://openalex.org/W4327550249","https://openalex.org/W4365444089","https://openalex.org/W4378745398","https://openalex.org/W4385245566","https://openalex.org/W4389126617","https://openalex.org/W4399041810","https://openalex.org/W4399391276","https://openalex.org/W6726873649","https://openalex.org/W6739901393","https://openalex.org/W6745537798","https://openalex.org/W6755207826","https://openalex.org/W6761987832","https://openalex.org/W6763868836","https://openalex.org/W6782527804","https://openalex.org/W6785123296","https://openalex.org/W6787696944","https://openalex.org/W6789365080","https://openalex.org/W6796581206","https://openalex.org/W6803993145","https://openalex.org/W6809747699","https://openalex.org/W6841184199","https://openalex.org/W6850142860"],"related_works":["https://openalex.org/W3000097931","https://openalex.org/W2354322770","https://openalex.org/W4237547500","https://openalex.org/W1570848052","https://openalex.org/W2373192430","https://openalex.org/W4239268388","https://openalex.org/W1537496349","https://openalex.org/W4243305035","https://openalex.org/W4390606538","https://openalex.org/W2095903272"],"abstract_inverted_index":{"Proteins":[0],"can":[1,98,124],"be":[2,99,125],"represented":[3],"in":[4,73,162],"different":[5,156],"data":[6,159],"forms,":[7],"including":[8,137],"sequence,":[9,52],"structure,":[10,53],"and":[11,19,54,71,82,117,141,152],"surface,":[12,72],"each":[13,88],"of":[14,78,158],"which":[15,74],"has":[16],"unique":[17],"advantages":[18],"certain":[20],"limitations.":[21],"It":[22],"is":[23,160],"promising":[24],"to":[25],"fuse":[26],"the":[27,47,75,109,113],"complementary":[28,48],"information":[29,49],"among":[30],"them.":[31],"In":[32],"this":[33],"work,":[34],"we":[35,61,103,131],"propose":[36,62],"a":[37,63,79,83],"framework":[38],"called":[39],"ProteinF3S":[40],"for":[41],"enzyme":[42,138,142,163],"function":[43,164],"prediction":[44],"that":[45,121,154],"fuses":[46],"across":[50],"protein":[51,69],"surface.":[55],"To":[56,127],"achieve":[57,104],"more":[58,95],"effective":[59,161],"fusion,":[60],"multi-scale":[64],"bidirectional":[65],"fusion":[66,106],"strategy":[67],"between":[68],"structure":[70,84,116],"hierarchical":[76],"features":[77,97,111,114],"surface":[80,118],"encoder":[81,85],"interact":[86],"with":[87,112],"other":[89],"bidirectionally.":[90],"Based":[91],"on":[92,135],"these":[93],"interactions,":[94],"distinctive":[96],"obtained.":[100],"After":[101],"that,":[102],"further":[105],"by":[107],"concatenating":[108],"sequence":[110],"containing":[115],"information,":[119],"so":[120],"better":[122],"performance":[123,151],"achieved.":[126],"validate":[128],"our":[129],"method,":[130],"conduct":[132],"extensive":[133],"experiments":[134],"tasks":[136],"reaction":[139],"classification":[140],"commission":[143],"number":[144],"prediction.":[145,165],"Our":[146],"method":[147],"achieves":[148],"new":[149],"state-of-the-art":[150],"shows":[153],"fusing":[155],"forms":[157]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
