{"id":"https://openalex.org/W4413104810","doi":"https://doi.org/10.1093/bib/bbaf394","title":"<i>DensePPI-2</i>: a bio-inspired update for sequence-based PPI prediction leveraging mutation rates","display_name":"<i>DensePPI-2</i>: a bio-inspired update for sequence-based PPI prediction leveraging mutation rates","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4413104810","doi":"https://doi.org/10.1093/bib/bbaf394","pmid":"https://pubmed.ncbi.nlm.nih.gov/40794945"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf394","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf394","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf394/63968491/bbaf394.pdf","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://academic.oup.com/bib/article-pdf/26/4/bbaf394/63968491/bbaf394.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056706283","display_name":"Tapas Chakraborty","orcid":"https://orcid.org/0000-0003-0026-6426"},"institutions":[{"id":"https://openalex.org/I170979836","display_name":"Jadavpur University","ror":"https://ror.org/02af4h012","country_code":"IN","type":"education","lineage":["https://openalex.org/I170979836"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Tapas Chakraborty","raw_affiliation_strings":["Department of Computer Science and Engineering, Jadavpur University , Kolkata, 700032 ,"],"raw_orcid":"https://orcid.org/0000-0003-0026-6426","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Jadavpur University , Kolkata, 700032 ,","institution_ids":["https://openalex.org/I170979836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002475277","display_name":"D Esker Paul","orcid":null},"institutions":[{"id":"https://openalex.org/I170979836","display_name":"Jadavpur University","ror":"https://ror.org/02af4h012","country_code":"IN","type":"education","lineage":["https://openalex.org/I170979836"]},{"id":"https://openalex.org/I4210145666","display_name":"Embedded Systems (United States)","ror":"https://ror.org/04742eh45","country_code":"US","type":"company","lineage":["https://openalex.org/I4210145666"]}],"countries":["IN","US"],"is_corresponding":false,"raw_author_name":"Debarati Paul","raw_affiliation_strings":["Department of Computer Science and Engineering, Jadavpur University , Kolkata, 700032 ,","Embedded Devices & Intelligent Systems, TCS Research & Innovation , Kolkata ,"],"raw_orcid":"https://orcid.org/0009-0007-5084-0314","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Jadavpur University , Kolkata, 700032 ,","institution_ids":["https://openalex.org/I170979836"]},{"raw_affiliation_string":"Embedded Devices & Intelligent Systems, TCS Research & Innovation , Kolkata ,","institution_ids":["https://openalex.org/I4210145666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077479201","display_name":"Aanzil Akram Halsana","orcid":"https://orcid.org/0000-0002-1107-1491"},"institutions":[{"id":"https://openalex.org/I170979836","display_name":"Jadavpur University","ror":"https://ror.org/02af4h012","country_code":"IN","type":"education","lineage":["https://openalex.org/I170979836"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Aanzil Akram Halsana","raw_affiliation_strings":["Department of Computer Science and Engineering, Jadavpur University , Kolkata, 700032 ,"],"raw_orcid":"https://orcid.org/0000-0002-1107-1491","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Jadavpur University , Kolkata, 700032 ,","institution_ids":["https://openalex.org/I170979836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055498019","display_name":"Anup Kumar Halder","orcid":"https://orcid.org/0000-0003-4825-1901"},"institutions":[{"id":"https://openalex.org/I108403487","display_name":"Warsaw University of Technology","ror":"https://ror.org/00y0xnp53","country_code":"PL","type":"education","lineage":["https://openalex.org/I108403487"]},{"id":"https://openalex.org/I111245572","display_name":"Indian Institute of Management Raipur","ror":"https://ror.org/05vqbh574","country_code":"IN","type":"education","lineage":["https://openalex.org/I111245572"]},{"id":"https://openalex.org/I268303160","display_name":"Medical University of Warsaw","ror":"https://ror.org/04p2y4s44","country_code":"PL","type":"education","lineage":["https://openalex.org/I268303160"]},{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]},{"id":"https://openalex.org/I59270414","display_name":"Indian Institute of Science Bangalore","ror":"https://ror.org/04dese585","country_code":"IN","type":"education","lineage":["https://openalex.org/I59270414"]},{"id":"https://openalex.org/I61553790","display_name":"University of Agricultural Sciences Raichur","ror":"https://ror.org/02tjcpt69","country_code":"IN","type":"education","lineage":["https://openalex.org/I61553790"]}],"countries":["IN","PL"],"is_corresponding":false,"raw_author_name":"Anup Kumar Halder","raw_affiliation_strings":["CeNT, University of Warsaw , 02-097 Warsaw ,","Department of Computer Science and Engineering, Indian Institute of Information Technology , Raichur, Karnataka ,"],"raw_orcid":"https://orcid.org/0000-0003-4825-1901","affiliations":[{"raw_affiliation_string":"CeNT, University of Warsaw , 02-097 Warsaw ,","institution_ids":["https://openalex.org/I108403487","https://openalex.org/I268303160","https://openalex.org/I4654613"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Indian Institute of Information Technology , Raichur, Karnataka ,","institution_ids":["https://openalex.org/I111245572","https://openalex.org/I59270414","https://openalex.org/I61553790"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043105133","display_name":"Subhadip Basu","orcid":"https://orcid.org/0000-0003-1780-0461"},"institutions":[{"id":"https://openalex.org/I170979836","display_name":"Jadavpur University","ror":"https://ror.org/02af4h012","country_code":"IN","type":"education","lineage":["https://openalex.org/I170979836"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Subhadip Basu","raw_affiliation_strings":["Department of Computer Science and Engineering, Jadavpur University , Kolkata, 700032 ,"],"raw_orcid":"https://orcid.org/0000-0003-1780-0461","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Jadavpur University , Kolkata, 700032 ,","institution_ids":["https://openalex.org/I170979836"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049571472","display_name":"Tapabrata Chakraborti","orcid":"https://orcid.org/0000-0002-5597-908X"},"institutions":[{"id":"https://openalex.org/I125680101","display_name":"Turing Institute","ror":"https://ror.org/02x2mw849","country_code":"GB","type":"facility","lineage":["https://openalex.org/I125680101"]},{"id":"https://openalex.org/I4210128584","display_name":"The Alan Turing Institute","ror":"https://ror.org/035dkdb55","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210128584"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Tapabrata Chakraborti","raw_affiliation_strings":["The Alan Turing Institute , London NW1 2DB, UK","University College London , London WC1E 6BT, UK"],"raw_orcid":"https://orcid.org/0000-0002-5597-908X","affiliations":[{"raw_affiliation_string":"The Alan Turing Institute , London NW1 2DB, UK","institution_ids":["https://openalex.org/I125680101","https://openalex.org/I4210128584"]},{"raw_affiliation_string":"University College London , London WC1E 6BT, UK","institution_ids":["https://openalex.org/I45129253"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5043105133","https://openalex.org/A5049571472"],"corresponding_institution_ids":["https://openalex.org/I125680101","https://openalex.org/I170979836","https://openalex.org/I4210128584","https://openalex.org/I45129253"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.409,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.60682115,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"26","issue":"4","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":0.9991000294685364,"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":0.9991000294685364,"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":0.9987000226974487,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9965999722480774,"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":0.6814210414886475},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5707963109016418},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5315622687339783},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.511840283870697},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.5012807846069336},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.48202788829803467},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4747845530509949},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4509085416793823},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.42899829149246216},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.4207271933555603},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.39240753650665283},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.318930983543396},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.2450934648513794},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23966673016548157},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18128836154937744},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09202295541763306}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6814210414886475},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5707963109016418},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5315622687339783},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.511840283870697},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.5012807846069336},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.48202788829803467},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4747845530509949},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4509085416793823},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.42899829149246216},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4207271933555603},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.39240753650665283},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.318930983543396},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.2450934648513794},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23966673016548157},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18128836154937744},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09202295541763306},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"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/bbaf394","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf394","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf394/63968491/bbaf394.pdf","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:40794945","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40794945","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:12341865","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12341865","pdf_url":null,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf394","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf394","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf394/63968491/bbaf394.pdf","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":[{"score":0.5299999713897705,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G731258544","display_name":null,"funder_award_id":"SUR/2022/002903","funder_id":"https://openalex.org/F4320334771","funder_display_name":"Science and Engineering Research Board"}],"funders":[{"id":"https://openalex.org/F4320306227","display_name":"Arthritis National Research Foundation","ror":"https://ror.org/03abbex33"},{"id":"https://openalex.org/F4320319990","display_name":"National Institute for Health and Care Research","ror":"https://ror.org/0187kwz08"},{"id":"https://openalex.org/F4320320286","display_name":"University College London","ror":"https://ror.org/02jx3x895"},{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320334771","display_name":"Science and Engineering Research Board","ror":"https://ror.org/03ffdsr55"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413104810.pdf","grobid_xml":"https://content.openalex.org/works/W4413104810.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1547142901","https://openalex.org/W1647597862","https://openalex.org/W1832794728","https://openalex.org/W2008840001","https://openalex.org/W2039473152","https://openalex.org/W2076710572","https://openalex.org/W2087612189","https://openalex.org/W2095867585","https://openalex.org/W2108134720","https://openalex.org/W2122863289","https://openalex.org/W2130687290","https://openalex.org/W2131562240","https://openalex.org/W2137786672","https://openalex.org/W2138865250","https://openalex.org/W2151412657","https://openalex.org/W2155723007","https://openalex.org/W2156125289","https://openalex.org/W2167821759","https://openalex.org/W2167869241","https://openalex.org/W2342374505","https://openalex.org/W2368923972","https://openalex.org/W2472351724","https://openalex.org/W2475686134","https://openalex.org/W2616246685","https://openalex.org/W2618265628","https://openalex.org/W2618529956","https://openalex.org/W2805806886","https://openalex.org/W2890911678","https://openalex.org/W2914020633","https://openalex.org/W2915536738","https://openalex.org/W2948793799","https://openalex.org/W2986210726","https://openalex.org/W3003217347","https://openalex.org/W3023539333","https://openalex.org/W3037788059","https://openalex.org/W3087512677","https://openalex.org/W3126039337","https://openalex.org/W3134169372","https://openalex.org/W4245668478","https://openalex.org/W4255855797","https://openalex.org/W4322730749","https://openalex.org/W4389742650","https://openalex.org/W6638589708","https://openalex.org/W6681108498","https://openalex.org/W6790156245","https://openalex.org/W6837882369"],"related_works":["https://openalex.org/W2946599741","https://openalex.org/W2593264178","https://openalex.org/W2136856901","https://openalex.org/W2368468053","https://openalex.org/W2058542300","https://openalex.org/W2043066834","https://openalex.org/W1564749278","https://openalex.org/W1741740882","https://openalex.org/W2035942032","https://openalex.org/W4390971102"],"abstract_inverted_index":{"Identifying":[0],"interactions":[1,191],"between":[2,39],"two":[3,41],"or":[4],"more":[5,100],"proteins":[6],"is":[7,55,110,128],"crucial":[8,111],"as":[9,35],"it":[10],"helps":[11],"understand":[12],"living":[13],"organisms'":[14],"cellular":[15],"behaviour":[16],"and":[17,52,68,72,106,120,192,230],"the":[18,31,46,82,92,113,118,151,159,170,175,199,215,218,225,231],"underlying":[19],"molecular":[20],"mechanisms":[21],"of":[22,44,49,84,103,122,148,177,217],"various":[23],"diseases.":[24],"However,":[25],"most":[26],"existing":[27,161],"computational":[28],"algorithms":[29],"in":[30,87],"field":[32],"model":[33,127,200],"this":[34],"a":[36,78,88,129],"binary":[37],"interaction":[38,60,179],"any":[40],"proteins,":[42],"instead":[43],"conserving":[45],"evolutionary":[47],"regions":[48],"protein":[50,89,104,142],"function":[51,121],"interactions.":[53,108],"This":[54,109],"important":[56],"for":[57,63,139,187,238],"predicting":[58,194],"potential":[59],"sites,":[61],"vital":[62],"drug":[64],"design,":[65],"target":[66],"identification,":[67],"understanding":[69],"disease":[70],"progression":[71],"pathogenic":[73],"mechanisms.":[74],"Position-aware":[75],"encoding":[76,135,222],"provides":[77],"way":[79],"to":[80,99],"incorporate":[81],"order":[83,115],"amino":[85],"acids":[86],"sequence":[90,114,134],"into":[91],"model,":[93],"thus":[94],"capturing":[95],"folding":[96],"patterns,":[97],"leading":[98],"accurate":[101],"predictions":[102],"structures":[105],"their":[107],"because":[112],"can":[116],"affect":[117],"structure":[119],"proteins.":[123],"The":[124,207,228],"proposed":[125],"DensePPI-2":[126,164,182],"novel":[130],"bio-inspired":[131,219],"substitution":[132,226],"matrix-based":[133],"with":[136],"deep":[137],"learning":[138],"identifying":[140,189],"interacting":[141],"pairs.":[143],"It":[144],"demonstrates":[145],"an":[146],"AUC":[147],"97.13%":[149],"on":[150,169,204,210],"S.":[152],"cerevisiae":[153],"dataset,":[154,173],"improving":[155],"by":[156],"1.4%":[157],"over":[158],"best":[160],"methods.":[162],"Furthermore,":[163],"outperforms":[165],"recent":[166],"sequence-based":[167],"approaches":[168],"human":[171],"benchmark":[172],"addressing":[174],"complexities":[176],"protein-protein":[178],"test":[180,212],"classes.":[181],"has":[183],"been":[184],"successfully":[185],"applied":[186],"(i)":[188],"pathogen-host":[190],"(ii)":[193],"near-residue-level":[195],"interaction,":[196],"even":[197],"though":[198],"was":[201],"not":[202],"trained":[203],"residue-level":[205],"data.":[206],"enhanced":[208],"performance":[209],"diverse":[211],"sets":[213],"proves":[214],"efficiency":[216],"sequence-to-image":[220],"colour":[221],"strategy":[223],"using":[224],"matrices.":[227],"dataset":[229],"developed":[232],"models":[233],"are":[234],"available":[235],"at":[236],"https://github.com/CMATERJU-BIOINFO/DensePPI-2":[237],"academic":[239],"use":[240],"only.":[241]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-08-12T00:00:00"}
