{"id":"https://openalex.org/W4412957094","doi":"https://doi.org/10.3389/fbinf.2025.1627836","title":"IDRdecoder: a machine learning approach for rational drug discovery toward intrinsically disordered regions","display_name":"IDRdecoder: a machine learning approach for rational drug discovery toward intrinsically disordered regions","publication_year":2025,"publication_date":"2025-07-18","ids":{"openalex":"https://openalex.org/W4412957094","doi":"https://doi.org/10.3389/fbinf.2025.1627836","pmid":"https://pubmed.ncbi.nlm.nih.gov/40756902"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1627836","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1627836","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers 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/10.3389/fbinf.2025.1627836","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5119209836","display_name":"Clara Shionyu-Mitusyama","orcid":null},"institutions":[{"id":"https://openalex.org/I194335595","display_name":"Nagahama Institute of Bio-Science and Technology","ror":"https://ror.org/03m5fme96","country_code":"JP","type":"education","lineage":["https://openalex.org/I194335595"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Clara Shionyu-Mitusyama","raw_affiliation_strings":["Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan","institution_ids":["https://openalex.org/I194335595"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Satoshi Ohmori","orcid":null},"institutions":[{"id":"https://openalex.org/I194335595","display_name":"Nagahama Institute of Bio-Science and Technology","ror":"https://ror.org/03m5fme96","country_code":"JP","type":"education","lineage":["https://openalex.org/I194335595"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Satoshi Ohmori","raw_affiliation_strings":["Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan","institution_ids":["https://openalex.org/I194335595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040973733","display_name":"S. Hirata","orcid":null},"institutions":[{"id":"https://openalex.org/I171494771","display_name":"Shiga University","ror":"https://ror.org/01vvhy971","country_code":"JP","type":"education","lineage":["https://openalex.org/I171494771"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Subaru Hirata","raw_affiliation_strings":["Faculty of Data Science, Shiga University 1-1-1 Banba, Hikone, Shiga, Japan"],"affiliations":[{"raw_affiliation_string":"Faculty of Data Science, Shiga University 1-1-1 Banba, Hikone, Shiga, Japan","institution_ids":["https://openalex.org/I171494771"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107431821","display_name":"Hirokazu Ishida","orcid":null},"institutions":[{"id":"https://openalex.org/I194335595","display_name":"Nagahama Institute of Bio-Science and Technology","ror":"https://ror.org/03m5fme96","country_code":"JP","type":"education","lineage":["https://openalex.org/I194335595"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hirokazu Ishida","raw_affiliation_strings":["Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan","institution_ids":["https://openalex.org/I194335595"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016135291","display_name":"Tsuyoshi Shirai","orcid":"https://orcid.org/0000-0002-2506-5738"},"institutions":[{"id":"https://openalex.org/I171494771","display_name":"Shiga University","ror":"https://ror.org/01vvhy971","country_code":"JP","type":"education","lineage":["https://openalex.org/I171494771"]},{"id":"https://openalex.org/I194335595","display_name":"Nagahama Institute of Bio-Science and Technology","ror":"https://ror.org/03m5fme96","country_code":"JP","type":"education","lineage":["https://openalex.org/I194335595"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Tsuyoshi Shirai","raw_affiliation_strings":["Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan","Faculty of Data Science, Shiga University 1-1-1 Banba, Hikone, Shiga, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan","institution_ids":["https://openalex.org/I194335595"]},{"raw_affiliation_string":"Faculty of Data Science, Shiga University 1-1-1 Banba, Hikone, Shiga, Japan","institution_ids":["https://openalex.org/I171494771"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5016135291"],"corresponding_institution_ids":["https://openalex.org/I171494771","https://openalex.org/I194335595"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.20288932,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"5","issue":null,"first_page":"1627836","last_page":"1627836"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9980999827384949,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.982699990272522,"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/autoencoder","display_name":"Autoencoder","score":0.7039828896522522},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.6773310899734497},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5727353692054749},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5365782976150513},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.5044156312942505},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.48836275935173035},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4631160497665405},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.41571077704429626},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3260291516780853},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.2967153787612915},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.24653387069702148},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.1918841302394867},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12406805157661438}],"concepts":[{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.7039828896522522},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.6773310899734497},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5727353692054749},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5365782976150513},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.5044156312942505},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.48836275935173035},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4631160497665405},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.41571077704429626},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3260291516780853},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.2967153787612915},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.24653387069702148},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.1918841302394867},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12406805157661438},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2025.1627836","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1627836","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40756902","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40756902","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:e78ce32e8bbd48a0ad0c1393d83bf39d","is_oa":true,"landing_page_url":"https://doaj.org/article/e78ce32e8bbd48a0ad0c1393d83bf39d","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":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11126149","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12313641","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1627836","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1627836","pdf_url":null,"source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.550000011920929}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":71,"referenced_works":["https://openalex.org/W1803223003","https://openalex.org/W1935389499","https://openalex.org/W1970469339","https://openalex.org/W1984921184","https://openalex.org/W2001635101","https://openalex.org/W2013354180","https://openalex.org/W2040452705","https://openalex.org/W2042244296","https://openalex.org/W2055043387","https://openalex.org/W2067080991","https://openalex.org/W2070030244","https://openalex.org/W2081648576","https://openalex.org/W2083258699","https://openalex.org/W2096525273","https://openalex.org/W2100495367","https://openalex.org/W2118608964","https://openalex.org/W2120167569","https://openalex.org/W2140128432","https://openalex.org/W2145653859","https://openalex.org/W2148161164","https://openalex.org/W2148271643","https://openalex.org/W2162268365","https://openalex.org/W2165581033","https://openalex.org/W2173732482","https://openalex.org/W2217901364","https://openalex.org/W2242464395","https://openalex.org/W2301705357","https://openalex.org/W2339242828","https://openalex.org/W2460324982","https://openalex.org/W2550670895","https://openalex.org/W2567785701","https://openalex.org/W2744614749","https://openalex.org/W2755742163","https://openalex.org/W2768477255","https://openalex.org/W2791796577","https://openalex.org/W2806884808","https://openalex.org/W2893323080","https://openalex.org/W2898210859","https://openalex.org/W2924607555","https://openalex.org/W2953384591","https://openalex.org/W2959496016","https://openalex.org/W2970588371","https://openalex.org/W2979572523","https://openalex.org/W2982547327","https://openalex.org/W3003257820","https://openalex.org/W3008295930","https://openalex.org/W3013875346","https://openalex.org/W3037826474","https://openalex.org/W3094246202","https://openalex.org/W3103145119","https://openalex.org/W3113748800","https://openalex.org/W3149136862","https://openalex.org/W3156113107","https://openalex.org/W3213738679","https://openalex.org/W4200540728","https://openalex.org/W4205440119","https://openalex.org/W4205773061","https://openalex.org/W4213160373","https://openalex.org/W4289274885","https://openalex.org/W4298140661","https://openalex.org/W4304084233","https://openalex.org/W4319598987","https://openalex.org/W4319871149","https://openalex.org/W4323036511","https://openalex.org/W4323565634","https://openalex.org/W4327550299","https://openalex.org/W4386936304","https://openalex.org/W4389298325","https://openalex.org/W4392937346","https://openalex.org/W4411392672","https://openalex.org/W6713134421"],"related_works":["https://openalex.org/W3013693939","https://openalex.org/W2566616303","https://openalex.org/W2159052453","https://openalex.org/W3131327266","https://openalex.org/W2734887215","https://openalex.org/W2803255133","https://openalex.org/W4297051394","https://openalex.org/W2752972570","https://openalex.org/W4386815338","https://openalex.org/W2145836866"],"abstract_inverted_index":{"IDRdecoder":[0],"is":[1],"the":[2,17],"first":[3],"application":[4],"for":[5,23,26],"predicting":[6],"drug":[7],"interaction":[8],"sites":[9],"and":[10,29],"ligands":[11],"in":[12,44],"IDR":[13],"sequences.":[14],"Analysis":[15],"of":[16],"prediction":[18],"results":[19],"revealed":[20],"characteristics":[21],"beneficial":[22],"IDR-drug":[24],"design;":[25],"instance,":[27],"Tyr":[28],"Ala":[30],"are":[31,42],"preferred":[32],"target":[33],"sites,":[34],"while":[35],"flexible":[36],"substructures,":[37],"such":[38],"as":[39],"alkyl":[40],"groups,":[41],"favored":[43],"ligand":[45],"molecules.":[46]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
