{"id":"https://openalex.org/W4412454098","doi":"https://doi.org/10.1093/bioinformatics/btaf191","title":"Accurate PROTAC-targeted degradation prediction with DegradeMaster","display_name":"Accurate PROTAC-targeted degradation prediction with DegradeMaster","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4412454098","doi":"https://doi.org/10.1093/bioinformatics/btaf191","pmid":"https://pubmed.ncbi.nlm.nih.gov/40662822"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf191","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf191","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i342/63745605/btaf191.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"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/bioinformatics/article-pdf/41/Supplement_1/i342/63745605/btaf191.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108390864","display_name":"Jie Liu","orcid":"https://orcid.org/0000-0002-2800-608X"},"institutions":[{"id":"https://openalex.org/I4210140852","display_name":"Centre for Cancer Biology","ror":"https://ror.org/03yg7hz06","country_code":"AU","type":"facility","lineage":["https://openalex.org/I107656453","https://openalex.org/I4210140852"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Jie Liu","raw_affiliation_strings":["South Australian Immunogenomics Cancer Institute (SAiGENCI), The University of Adelaide , Adelaide, South Australia 5005,"],"affiliations":[{"raw_affiliation_string":"South Australian Immunogenomics Cancer Institute (SAiGENCI), The University of Adelaide , Adelaide, South Australia 5005,","institution_ids":["https://openalex.org/I4210140852"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006204612","display_name":"Michael J. Roy","orcid":"https://orcid.org/0000-0003-0198-9108"},"institutions":[{"id":"https://openalex.org/I4210140852","display_name":"Centre for Cancer Biology","ror":"https://ror.org/03yg7hz06","country_code":"AU","type":"facility","lineage":["https://openalex.org/I107656453","https://openalex.org/I4210140852"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Michael J Roy","raw_affiliation_strings":["South Australian Immunogenomics Cancer Institute (SAiGENCI), The University of Adelaide , Adelaide, South Australia 5005,"],"affiliations":[{"raw_affiliation_string":"South Australian Immunogenomics Cancer Institute (SAiGENCI), The University of Adelaide , Adelaide, South Australia 5005,","institution_ids":["https://openalex.org/I4210140852"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087988571","display_name":"Luke Isbel","orcid":"https://orcid.org/0000-0002-5270-4347"},"institutions":[{"id":"https://openalex.org/I4210140852","display_name":"Centre for Cancer Biology","ror":"https://ror.org/03yg7hz06","country_code":"AU","type":"facility","lineage":["https://openalex.org/I107656453","https://openalex.org/I4210140852"]},{"id":"https://openalex.org/I5681781","display_name":"The University of Adelaide","ror":"https://ror.org/00892tw58","country_code":"AU","type":"education","lineage":["https://openalex.org/I5681781"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Luke Isbel","raw_affiliation_strings":["Adelaide Centre for Epigenetics, The University of Adelaide , Adelaide, South Australia 5005,","South Australian Immunogenomics Cancer Institute (SAiGENCI), The University of Adelaide , Adelaide, South Australia 5005,"],"affiliations":[{"raw_affiliation_string":"Adelaide Centre for Epigenetics, The University of Adelaide , Adelaide, South Australia 5005,","institution_ids":["https://openalex.org/I5681781"]},{"raw_affiliation_string":"South Australian Immunogenomics Cancer Institute (SAiGENCI), The University of Adelaide , Adelaide, South Australia 5005,","institution_ids":["https://openalex.org/I4210140852"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063409460","display_name":"Fuyi Li","orcid":"https://orcid.org/0000-0001-5216-3213"},"institutions":[{"id":"https://openalex.org/I4210140852","display_name":"Centre for Cancer Biology","ror":"https://ror.org/03yg7hz06","country_code":"AU","type":"facility","lineage":["https://openalex.org/I107656453","https://openalex.org/I4210140852"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Fuyi Li","raw_affiliation_strings":["South Australian Immunogenomics Cancer Institute (SAiGENCI), The University of Adelaide , Adelaide, South Australia 5005,"],"affiliations":[{"raw_affiliation_string":"South Australian Immunogenomics Cancer Institute (SAiGENCI), The University of Adelaide , Adelaide, South Australia 5005,","institution_ids":["https://openalex.org/I4210140852"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5108390864"],"corresponding_institution_ids":["https://openalex.org/I4210140852"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":6.1004,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.96707929,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"41","issue":"Supplement_1","first_page":"i342","last_page":"i351"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12534","display_name":"Protein Degradation and Inhibitors","score":1.0,"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/T12534","display_name":"Protein Degradation and Inhibitors","score":1.0,"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/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.9919000267982483,"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/T10649","display_name":"Multiple Myeloma Research and Treatments","score":0.9692000150680542,"subfield":{"id":"https://openalex.org/subfields/2720","display_name":"Hematology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7071659564971924},{"id":"https://openalex.org/keywords/pooling","display_name":"Pooling","score":0.650196373462677},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5282142758369446},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5253400206565857},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4981961250305176},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.48655739426612854},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.480340838432312},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.43782657384872437},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4119393229484558},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.19542574882507324},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.16542816162109375},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10206678509712219}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7071659564971924},{"id":"https://openalex.org/C70437156","wikidata":"https://www.wikidata.org/wiki/Q7228652","display_name":"Pooling","level":2,"score":0.650196373462677},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5282142758369446},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5253400206565857},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4981961250305176},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.48655739426612854},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.480340838432312},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.43782657384872437},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4119393229484558},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.19542574882507324},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.16542816162109375},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10206678509712219}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D044767","descriptor_name":"Ubiquitin-Protein Ligases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059748","descriptor_name":"Proteolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059748","descriptor_name":"Proteolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059748","descriptor_name":"Proteolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059748","descriptor_name":"Proteolysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf191","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf191","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i342/63745605/btaf191.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40662822","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40662822","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12261415","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12261415","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf191","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf191","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i342/63745605/btaf191.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3684951744","display_name":null,"funder_award_id":"2041439","funder_id":"https://openalex.org/F4320334705","funder_display_name":"National Health and Medical Research Council"}],"funders":[{"id":"https://openalex.org/F4320315885","display_name":"Australian Government","ror":"https://ror.org/0314h5y94"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412454098.pdf","grobid_xml":"https://content.openalex.org/works/W4412454098.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1606340521","https://openalex.org/W1678356000","https://openalex.org/W2028629022","https://openalex.org/W2044834685","https://openalex.org/W2066713758","https://openalex.org/W2130479394","https://openalex.org/W2151683271","https://openalex.org/W2200017991","https://openalex.org/W2237051895","https://openalex.org/W2589026097","https://openalex.org/W2597078857","https://openalex.org/W2903964626","https://openalex.org/W2908747386","https://openalex.org/W2912114516","https://openalex.org/W2944303665","https://openalex.org/W2948220248","https://openalex.org/W3177828909","https://openalex.org/W4205379795","https://openalex.org/W4225687325","https://openalex.org/W4309650743","https://openalex.org/W4310760182","https://openalex.org/W4312064763","https://openalex.org/W4375855261","https://openalex.org/W4383187595","https://openalex.org/W4385931734","https://openalex.org/W4387930985","https://openalex.org/W4402170913","https://openalex.org/W4402625837","https://openalex.org/W6637404493"],"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/W2953234277","https://openalex.org/W2669956259","https://openalex.org/W4249005693","https://openalex.org/W4392946183","https://openalex.org/W4405887298"],"abstract_inverted_index":{"The":[0],"source":[1],"code":[2],"and":[3,9],"datasets":[4],"are":[5],"available":[6],"at":[7],"https://github.com/ABILiLab/DegradeMaster":[8],"https://zenodo.org/records/14715718.":[10]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
