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The IDRs can be divided into long disordered regions (LDRs) and short disordered regions (SDRs) according to their lengths. In previous studies, most computational methods ignored the differences between LDRs and SDRs, and therefore failed to capture the different patterns of LDRs and SDRs. In this study, we propose IDP-EDL, an ensemble of three predictors. The component predictors were first built based on pretrained protein language model and applied task-specific fine-tuning for short, long, and generic disordered regions. A meta predictor was then trained to integrate three task-specific predictors into the final predictor. The results of experiments show that task-specific supervised fine-tuning can capture the different features of LDRs and SDRs and IDP-EDL can achieve stable performance on datasets with different ratios of LDRs and SDRs. More importantly, IDP-EDL can reach or even surpass state-of-the-art performance than other existing predictors on independent test sets. IDP-EDL is available at https:\/\/github.com\/joestarXjx\/IDP-EDL.<\/jats:p>","DOI":"10.1093\/bib\/bbaf182","type":"journal-article","created":{"date-parts":[[2025,4,21]],"date-time":"2025-04-21T03:57:00Z","timestamp":1745207820000},"source":"Crossref","is-referenced-by-count":2,"title":["IDP-EDL: enhancing intrinsically disordered protein prediction by combining protein language model and ensemble deep learning"],"prefix":"10.1093","volume":"26","author":[{"given":"Junxi","family":"Xie","sequence":"first","affiliation":[{"name":"College of Big Data and Internet, Shenzhen Technology University , 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118 ,","place":["China"]}]},{"given":"Xiaopeng","family":"Jin","sequence":"additional","affiliation":[{"name":"College of Big Data and Internet, Shenzhen Technology University , 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118 ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0579-1716","authenticated-orcid":false,"given":"Hang","family":"Wei","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Xidian University , South Campus: 266 Xinglong Section of Xifeng Road, Xi\u2019an, Shaanxi 710126, North Campus: No. 2 South Taibai Road, Xi\u2019an, Shaanxi 710071 ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-6090-3030","authenticated-orcid":false,"given":"SaiSai","family":"Sun","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Xidian University , South Campus: 266 Xinglong Section of Xifeng Road, Xi\u2019an, Shaanxi 710126, North Campus: No. 2 South Taibai Road, Xi\u2019an, Shaanxi 710071 ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-0888-6575","authenticated-orcid":false,"given":"Yumeng","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Big Data and Internet, Shenzhen Technology University , 3002 Lantian Road, Pingshan District, Shenzhen, Guangdong 518118 ,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,4,21]]},"reference":[{"key":"2025042023564306100_ref1","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1038\/nrm1589","article-title":"Intrinsically unstructured proteins and their functions","volume":"6","author":"Jane Dyson","year":"2005","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2025042023564306100_ref2","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1016\/S0022-2836(02)00969-5","article-title":"Intrinsic disorder in cell-signaling and cancer-associated proteins","volume":"323","author":"Iakoucheva","year":"2002","journal-title":"J Mol Biol"},{"key":"2025042023564306100_ref3","doi-asserted-by":"crossref","first-page":"D219","DOI":"10.1093\/nar\/gkw1056","article-title":"Disprot 7.0: a major update of the database of disordered proteins","volume":"45","author":"Piovesan","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2025042023564306100_ref4","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s12915-023-01803-y","article-title":"Disoflag: accurate prediction of protein intrinsic disorder and its functions using graph-based interaction protein language model","volume":"22","author":"Pang","year":"2024","journal-title":"BMC Biol"},{"key":"2025042023564306100_ref5","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1146\/annurev.biophys.37.032807.125924","article-title":"Intrinsically disordered proteins in human diseases: introducing the d2 concept","volume":"37","author":"Uversky","year":"2008","journal-title":"Annu Rev Biophys"},{"key":"2025042023564306100_ref6","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1002\/prot.20750","article-title":"Assessing protein disorder and induced folding","volume":"62","author":"Receveur-Br\u00e9chot","year":"2006","journal-title":"Proteins"},{"key":"2025042023564306100_ref7","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1016\/j.jmr.2013.11.011","article-title":"Nmr contributions to structural dynamics studies of intrinsically disordered proteins","volume":"241","author":"Konrat","year":"2014","journal-title":"J Magn Reson"},{"key":"2025042023564306100_ref8","doi-asserted-by":"publisher","first-page":"D315","DOI":"10.1093\/nar\/gku982","article-title":"Mobidb 2.0: an improved database of intrinsically disordered and mobile proteins","volume":"43","author":"Potenza","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2025042023564306100_ref9","doi-asserted-by":"publisher","first-page":"D269","DOI":"10.1093\/nar\/gkz975","article-title":"Disprot: intrinsic protein disorder annotation in 2020","volume":"48","author":"Hatos","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2025042023564306100_ref10","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1038\/s42256-022-00457-9","article-title":"Learning functional properties of proteins with language models. 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