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Journal Articles
2026
1.
Nugnes M V; Bouhraoua K E A; Zoubiri M; Pancsa R; Fichó E; Monzon A M; Melo A M; Salladini E; Leonardi E; Quaglia F; Nasiribavil D; Ghafouri H; Julien G; Pasche E; Ruch P; Rijen P V; Dobson L; Schiavina M; Cordero T; Kálmán Z E; Castro X; Iglesias V; Reményi I; Mehdiabadi M; Erdős G; Dosztányi Z; Tompa P; Piovesan D; Tosatto S C E; Aspromonte M C
DisProt in 2026: enhancing intrinsically disordered proteins accessibility, deposition, and annotation Journal Article
In: Nucleic Acids Research, vol. 54, no. D1, pp. D383-D392, 2026, (Cited by: 4; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:105027748200,
title = {DisProt in 2026: enhancing intrinsically disordered proteins accessibility, deposition, and annotation},
author = {Maria Victoria Nugnes and Kamel Eddine Adel Bouhraoua and Mehdi Zoubiri and Rita Pancsa and Erzsébet Fichó and Alexander M Monzon and Ana M Melo and Edoardo Salladini and Emanuela Leonardi and Federica Quaglia and Daniyal Nasiribavil and Hamidreza Ghafouri and Gobeill Julien and Emilie Pasche and Patrick Ruch and Paul Van Rijen and László Dobson and Marco Schiavina and Trinidad Cordero and Zsófia E Kálmán and Ximena Castro and Valentín Iglesias and István Reményi and Mahta Mehdiabadi and Gábor Erdős and Zsuzsanna Dosztányi and Peter Tompa and Damiano Piovesan and Silvio C. E Tosatto and Maria Cristina Aspromonte},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-105027748200&origin=inward},
doi = {10.1093/nar/gkaf1175},
year = {2026},
date = {2026-01-01},
journal = {Nucleic Acids Research},
volume = {54},
number = {D1},
pages = {D383-D392},
publisher = {Oxford University Press},
abstract = {© 2025 The Author(s). Published by Oxford University Press.DisProt (https://disprot.org/) is an open database integrating experimental evidence on intrinsically disordered proteins (IDPs), intrinsically disordered regions (IDRs), and their functions. Over the past two years, the database has grown over 20%, now comprising 3201 IDPs and 13 347 pieces of evidence, including over 1500 new structural state annotations and >1300 new function annotations. DisProt has systematically adopted the Minimum Information About Disorder Experiments (MIADE) guidelines, more than doubling annotations with experimental details and improving the interpretability of disorder-related experiments. The website has evolved into a hybrid knowledgebase and deposition system, introducing a Deposition Page that allows direct submissions by external users. Through BLAST-based homology propagation in MobiDB, DisProt disorder regions and linear interacting peptides have been extended from hundreds to hundreds of thousands of proteins across >11 000 organisms. This new release marks a paradigm shift by integrating computational predictions as valid evidence and introducing major updates and restructuring of the IDP Ontology, enhancing accuracy, interoperability, and semantic clarity. DisProt continues to support community engagement through training resources together with DisTriage, an AI-based literature triage tool, providing curators with regularly updated lists of prioritized publications.},
note = {Cited by: 4; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© 2025 The Author(s). Published by Oxford University Press.DisProt (https://disprot.org/) is an open database integrating experimental evidence on intrinsically disordered proteins (IDPs), intrinsically disordered regions (IDRs), and their functions. Over the past two years, the database has grown over 20%, now comprising 3201 IDPs and 13 347 pieces of evidence, including over 1500 new structural state annotations and >1300 new function annotations. DisProt has systematically adopted the Minimum Information About Disorder Experiments (MIADE) guidelines, more than doubling annotations with experimental details and improving the interpretability of disorder-related experiments. The website has evolved into a hybrid knowledgebase and deposition system, introducing a Deposition Page that allows direct submissions by external users. Through BLAST-based homology propagation in MobiDB, DisProt disorder regions and linear interacting peptides have been extended from hundreds to hundreds of thousands of proteins across >11 000 organisms. This new release marks a paradigm shift by integrating computational predictions as valid evidence and introducing major updates and restructuring of the IDP Ontology, enhancing accuracy, interoperability, and semantic clarity. DisProt continues to support community engagement through training resources together with DisTriage, an AI-based literature triage tool, providing curators with regularly updated lists of prioritized publications.
2.
Mehdiabadi M; Conte A D; Nugnes M V; Aspromonte M C; Tosatto S C E; Piovesan D
Critical Assessment of Protein Intrinsic Disorder Round 3 – Predicting Disorder in the Era of Protein Language Models Journal Article
In: Proteins: Structure, Function and Bioinformatics, vol. 94, no. 1, pp. 414-424, 2026, (Cited by: 3; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:105014118997,
title = {Critical Assessment of Protein Intrinsic Disorder Round 3 - Predicting Disorder in the Era of Protein Language Models},
author = {Mahta Mehdiabadi and Alessio Del Conte and Maria Victoria Nugnes and Maria Cristina Aspromonte and Silvio C. E. Tosatto and Damiano Piovesan},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-105014118997&origin=inward},
doi = {10.1002/prot.70045},
year = {2026},
date = {2026-01-01},
journal = {Proteins: Structure, Function and Bioinformatics},
volume = {94},
number = {1},
pages = {414-424},
publisher = {John Wiley and Sons Inc},
abstract = {© 2025 The Author(s). PROTEINS: Structure, Function, and Bioinformatics published by Wiley Periodicals LLC.Intrinsic disorder (ID) in proteins is a complex phenomenon, encompassing a continuum from entirely disordered regions to structured domains with flexible segments. The absence of a ground truth for all forms of disorder, combined with the possibility of structural transitions between ordered and disordered states under specific conditions, makes accurate prediction of ID especially challenging. The Critical Assessment of Protein Intrinsic Disorder (CAID) evaluates ID prediction methods using diverse benchmarks derived from DisProt, a manually curated database of experimentally validated annotations. This paper presents findings from the third round (CAID3), in which 24 new methods were assessed along with the predictors from previous rounds. Compared to CAID2, the top-performing methods in CAID3 demonstrated significant gains in average precision: over 31% improvement in predicting linker regions, and 15% in disorder prediction. This round introduces a new binding sub-challenge focused on identifying binding regions within known IDR boundaries. The results indicate that this task remains challenging, highlighting the potential for improvement. The top-performing methods in CAID3 are mostly new and commonly used embeddings from protein language models (pLMs), underscoring the growing impact of pLMs in tackling the complexities of disordered proteins and advancing ID prediction.},
note = {Cited by: 3; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© 2025 The Author(s). PROTEINS: Structure, Function, and Bioinformatics published by Wiley Periodicals LLC.Intrinsic disorder (ID) in proteins is a complex phenomenon, encompassing a continuum from entirely disordered regions to structured domains with flexible segments. The absence of a ground truth for all forms of disorder, combined with the possibility of structural transitions between ordered and disordered states under specific conditions, makes accurate prediction of ID especially challenging. The Critical Assessment of Protein Intrinsic Disorder (CAID) evaluates ID prediction methods using diverse benchmarks derived from DisProt, a manually curated database of experimentally validated annotations. This paper presents findings from the third round (CAID3), in which 24 new methods were assessed along with the predictors from previous rounds. Compared to CAID2, the top-performing methods in CAID3 demonstrated significant gains in average precision: over 31% improvement in predicting linker regions, and 15% in disorder prediction. This round introduces a new binding sub-challenge focused on identifying binding regions within known IDR boundaries. The results indicate that this task remains challenging, highlighting the potential for improvement. The top-performing methods in CAID3 are mostly new and commonly used embeddings from protein language models (pLMs), underscoring the growing impact of pLMs in tackling the complexities of disordered proteins and advancing ID prediction.
3.
Mehdiabadi M; Tosatto S C E; Piovesan D
Modeling intrinsically disordered regions from AlphaFold2 to AlphaFold3 Journal Article
In: Protein Science, vol. 35, no. 1, 2026, (Cited by: 0; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:105026115828,
title = {Modeling intrinsically disordered regions from AlphaFold2 to AlphaFold3},
author = {Mahta Mehdiabadi and Silvio C. E. Tosatto and Damiano Piovesan},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-105026115828&origin=inward},
doi = {10.1002/pro.70426},
year = {2026},
date = {2026-01-01},
journal = {Protein Science},
volume = {35},
number = {1},
publisher = {John Wiley and Sons Inc},
abstract = {© 2025 The Protein Society.AlphaFold2 has demonstrated a remarkable success in predicting the structures of globular proteins and folded domains with near-experimental accuracy. However, it typically represents intrinsically disordered regions (IDRs), protein segments that lack a stable 3D structure under physiological conditions, as long extended loops that appear to float around the structured core. While AlphaFold2's static prediction cannot capture the conformational heterogeneity and the dynamic nature of IDRs, it performs well in predicting IDRs from sequence. AlphaFold3 introduces significant architectural and training modifications over its predecessor, including the use of cross-distillation aimed at reducing structural hallucinations in disordered regions. In this study, we look into how these models differ in representing IDRs. We evaluate the performance of AlphaFold3 and AlphaFold2 on disorder prediction, using the CAID3 benchmark. Our analysis shows that AlphaFold3 does not outperform AlphaFold2 in this benchmark. We observe that solvent accessibility remains a robust and consistent proxy for predicting intrinsic disorder across both models. However, changes in the predicted secondary structure content and pLDDT scores lead to different interpretations of disorder. Overall, our findings suggest that AlphaFold2 remains the preferred choice for identifying intrinsically disordered regions, as it avoids structural hallucinations while providing predictions comparable to those of AlphaFold3.},
note = {Cited by: 0; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© 2025 The Protein Society.AlphaFold2 has demonstrated a remarkable success in predicting the structures of globular proteins and folded domains with near-experimental accuracy. However, it typically represents intrinsically disordered regions (IDRs), protein segments that lack a stable 3D structure under physiological conditions, as long extended loops that appear to float around the structured core. While AlphaFold2’s static prediction cannot capture the conformational heterogeneity and the dynamic nature of IDRs, it performs well in predicting IDRs from sequence. AlphaFold3 introduces significant architectural and training modifications over its predecessor, including the use of cross-distillation aimed at reducing structural hallucinations in disordered regions. In this study, we look into how these models differ in representing IDRs. We evaluate the performance of AlphaFold3 and AlphaFold2 on disorder prediction, using the CAID3 benchmark. Our analysis shows that AlphaFold3 does not outperform AlphaFold2 in this benchmark. We observe that solvent accessibility remains a robust and consistent proxy for predicting intrinsic disorder across both models. However, changes in the predicted secondary structure content and pLDDT scores lead to different interpretations of disorder. Overall, our findings suggest that AlphaFold2 remains the preferred choice for identifying intrinsically disordered regions, as it avoids structural hallucinations while providing predictions comparable to those of AlphaFold3.
2025
4.
Mehdiabadi M; Blum M; Tesei G; Bulow S; Lindorff-Larsen K; Tosatto S C E; Piovesan D
MobiDB-lite 4.0: faster prediction of intrinsic protein disorder and structural compactness Journal Article
In: Bioinformatics, vol. 41, no. 5, 2025, (Cited by: 0; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:105007010286,
title = {MobiDB-lite 4.0: faster prediction of intrinsic protein disorder and structural compactness},
author = {Mahta Mehdiabadi and Matthias Blum and Giulio Tesei and Soren Bulow and Kresten Lindorff-Larsen and Silvio C. E. Tosatto and Damiano Piovesan},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-105007010286&origin=inward},
doi = {10.1093/bioinformatics/btaf297},
year = {2025},
date = {2025-01-01},
journal = {Bioinformatics},
volume = {41},
number = {5},
publisher = {Oxford University Press},
abstract = {© The Author(s) 2025. Published by Oxford University Press.Motivation: In recent years, many disorder predictors have been developed to identify intrinsically disordered regions (IDRs) in proteins, achieving high accuracy. However, it may be difficult to interpret differences in predictions across methods. Consensus methods offer a simple solution, highlighting reliable predictions while filtering out uncertain positions. Here, we present a new version of MobiDB-lite, a consensus method designed to predict long IDRs and classify them based on compositional biases and conformational properties. Results: MobiDB-lite 4.0 pipeline was optimized to be ten times faster than the previous version. It now provides compactness annotations based on predicted apparent scaling exponent. The newly added features and disorder subclassifications allow the users to get a comprehensive insight into the protein’s function and characteristics. MobiDB-lite 4.0 is integrated into the MobiDB and DisProt databases. A version without the compactness predictor is integrated into InterProScan, propagating MobiDB-lite annotations to UniProtKB. Availability and implementation: The MobiDB-lite 4.0 source code and a Docker container are available from the GitHub repository: https://github.com/BioComputingUP/MobiDB-lite.},
note = {Cited by: 0; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© The Author(s) 2025. Published by Oxford University Press.Motivation: In recent years, many disorder predictors have been developed to identify intrinsically disordered regions (IDRs) in proteins, achieving high accuracy. However, it may be difficult to interpret differences in predictions across methods. Consensus methods offer a simple solution, highlighting reliable predictions while filtering out uncertain positions. Here, we present a new version of MobiDB-lite, a consensus method designed to predict long IDRs and classify them based on compositional biases and conformational properties. Results: MobiDB-lite 4.0 pipeline was optimized to be ten times faster than the previous version. It now provides compactness annotations based on predicted apparent scaling exponent. The newly added features and disorder subclassifications allow the users to get a comprehensive insight into the protein’s function and characteristics. MobiDB-lite 4.0 is integrated into the MobiDB and DisProt databases. A version without the compactness predictor is integrated into InterProScan, propagating MobiDB-lite annotations to UniProtKB. Availability and implementation: The MobiDB-lite 4.0 source code and a Docker container are available from the GitHub repository: https://github.com/BioComputingUP/MobiDB-lite.
5.
Piovesan D; Conte A D; Mehdiabadi M; Aspromonte M C; Blum M; Tesei G; Bülow S; Lindorff-Larsen K; Tosatto S C E
MOBIDB in 2025: integrating ensemble properties and function annotations for intrinsically disordered proteins Journal Article
In: Nucleic Acids Research, vol. 53, no. D1, pp. D495-D503, 2025, (Cited by: 34; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:85213063415,
title = {MOBIDB in 2025: integrating ensemble properties and function annotations for intrinsically disordered proteins},
author = {Damiano Piovesan and Alessio Del Conte and Mahta Mehdiabadi and Maria Cristina Aspromonte and Matthias Blum and Giulio Tesei and Sören Bülow and Kresten Lindorff-Larsen and Silvio C. E. Tosatto},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-85213063415&origin=inward},
doi = {10.1093/nar/gkae969},
year = {2025},
date = {2025-01-01},
journal = {Nucleic Acids Research},
volume = {53},
number = {D1},
pages = {D495-D503},
publisher = {Oxford University Press},
abstract = {© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.The MobiDB database (URL: https://mobidb.org/) aims to provide structural and functional information about intrinsic protein disorder, aggregating annotations from the literature, experimental data, and predictions for all known protein sequences. Here, we describe the improvements made to our resource to capture more information, simplify access to the aggregated data, and increase documentation of all MobiDB features. Compared to the previous release, all underlying pipeline modules were updated. The prediction module is ten times faster and can detect if a predicted disordered region is structurally extended or compact. The PDB component is now able to process large cryo-EM structures extending the number of processed entries. The entry page has been restyled to highlight functional aspects of disorder and all graphical modules have been completely reimplemented for better flexibility and faster rendering. The server has been improved to optimise bulk downloads. Annotation provenance has been standardised by adopting ECO terms. Finally, we propagated disorder function (IDPO and GO terms) from the DisProt database exploiting sequence similarity and protein embeddings. These improvements, along with the addition of comprehensive training material, offer a more intuitive interface and novel functional knowledge about intrinsic disorder.},
note = {Cited by: 34; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.The MobiDB database (URL: https://mobidb.org/) aims to provide structural and functional information about intrinsic protein disorder, aggregating annotations from the literature, experimental data, and predictions for all known protein sequences. Here, we describe the improvements made to our resource to capture more information, simplify access to the aggregated data, and increase documentation of all MobiDB features. Compared to the previous release, all underlying pipeline modules were updated. The prediction module is ten times faster and can detect if a predicted disordered region is structurally extended or compact. The PDB component is now able to process large cryo-EM structures extending the number of processed entries. The entry page has been restyled to highlight functional aspects of disorder and all graphical modules have been completely reimplemented for better flexibility and faster rendering. The server has been improved to optimise bulk downloads. Annotation provenance has been standardised by adopting ECO terms. Finally, we propagated disorder function (IDPO and GO terms) from the DisProt database exploiting sequence similarity and protein embeddings. These improvements, along with the addition of comprehensive training material, offer a more intuitive interface and novel functional knowledge about intrinsic disorder.
