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Journal Articles
2025
1.
Han K; Song S; Pak M; Kim C; Ri C; Conte A D; Piovesan D
PredIDR: Accurate prediction of protein intrinsic disorder regions using deep convolutional neural network Journal Article
In: International Journal of Biological Macromolecules, vol. 284, 2025, (Cited by: 0; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:85210122158,
title = {PredIDR: Accurate prediction of protein intrinsic disorder regions using deep convolutional neural network},
author = {Kun-Sop Han and Se-Ryong Song and Myong-hyon Pak and Chol-Song Kim and Chol-Pyok Ri and Alessio Del Conte and Damiano Piovesan},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-85210122158&origin=inward},
doi = {10.1016/j.ijbiomac.2024.137665},
year = {2025},
date = {2025-01-01},
journal = {International Journal of Biological Macromolecules},
volume = {284},
publisher = {Elsevier B.V.},
abstract = {© 2024 Elsevier B.V.The involvement of protein intrinsic disorder in essential biological processes, it is well known in structural biology. However, experimental methods for detecting intrinsic structural disorder and directly measuring highly dynamic behavior of protein structure are limited. To address this issue, several computational methods to predict intrinsic disorder from protein sequences were developed and their performance is evaluated by the Critical Assessment of protein Intrinsic Disorder (CAID). In this paper, we describe a new computational method, PredIDR, which provides accurate prediction of intrinsically disordered regions in proteins, mimicking experimental X-ray missing residues. Indeed, missing residues in Protein Data Bank (PDB) were used as positive examples to train a deep convolutional neural network which produces two types of output for short and long regions. PredIDR took part in the second round of CAID and was as accurate as the top state-of-the-art IDR prediction methods. PredIDR can be freely used through the CAID Prediction Portal available at https://caid.idpcentral.org/portal or downloaded as a Singularity container from https://biocomputingup.it/shared/caid-predictors/.},
note = {Cited by: 0; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© 2024 Elsevier B.V.The involvement of protein intrinsic disorder in essential biological processes, it is well known in structural biology. However, experimental methods for detecting intrinsic structural disorder and directly measuring highly dynamic behavior of protein structure are limited. To address this issue, several computational methods to predict intrinsic disorder from protein sequences were developed and their performance is evaluated by the Critical Assessment of protein Intrinsic Disorder (CAID). In this paper, we describe a new computational method, PredIDR, which provides accurate prediction of intrinsically disordered regions in proteins, mimicking experimental X-ray missing residues. Indeed, missing residues in Protein Data Bank (PDB) were used as positive examples to train a deep convolutional neural network which produces two types of output for short and long regions. PredIDR took part in the second round of CAID and was as accurate as the top state-of-the-art IDR prediction methods. PredIDR can be freely used through the CAID Prediction Portal available at https://caid.idpcentral.org/portal or downloaded as a Singularity container from https://biocomputingup.it/shared/caid-predictors/.
2.
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: 1; 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: 1; 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.
2024
3.
Attafi O A; Clementel D; Kyritsis K; Capriotti E; Farrell G; Fragkouli S; Castro L J; Hatos A; Lenaerts T; Mazurenko S; Mozaffari S; Pradelli F; Ruch P; Savojardo C; Turina P; Zambelli F; Piovesan D; Monzon A M; Psomopoulos F; Tosatto S C E
DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology Journal Article
In: GigaScience, vol. 13, 2024, (Cited by: 0; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:85212459848,
title = {DOME Registry: implementing community-wide recommendations for reporting supervised machine learning in biology},
author = {Omar Abdelghani Attafi and Damiano Clementel and Konstantinos Kyritsis and Emidio Capriotti and Gavin Farrell and Styliani-Christina Fragkouli and Leyla Jael Castro and András Hatos and Tom Lenaerts and Stanislav Mazurenko and Soroush Mozaffari and Franco Pradelli and Patrick Ruch and Castrense Savojardo and Paola Turina and Federico Zambelli and Damiano Piovesan and Alexander Miguel Monzon and Fotis Psomopoulos and Silvio C. E. Tosatto},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-85212459848&origin=inward},
doi = {10.1093/gigascience/giae094},
year = {2024},
date = {2024-01-01},
journal = {GigaScience},
volume = {13},
publisher = {Oxford University Press},
abstract = {© The Author(s) 2024. Published by Oxford University Press GigaScience.Supervised machine learning (ML) is used extensively in biology and deserves closer scrutiny. The Data Optimization Model Evaluation (DOME) recommendations aim to enhance the validation and reproducibility of ML research by establishing standards for key aspects such as data handling and processing, optimization, evaluation, and model interpretability. The recommendations help to ensure that key details are reported transparently by providing a structured set of questions. Here, we introduce the DOME registry (URL: registry.dome-ml.org), a database that allows scientists to manage and access comprehensive DOME-related information on published ML studies. The registry uses external resources like ORCID, APICURON, and the Data Stewardship Wizard to streamline the annotation process and ensure comprehensive documentation. By assigning unique identifiers and DOME scores to publications, the registry fosters a standardized evaluation of ML methods. Future plans include continuing to grow the registry through community curation, improving the DOME score definition and encouraging publishers to adopt DOME standards, and promoting transparency and reproducibility of ML in the life sciences.},
note = {Cited by: 0; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© The Author(s) 2024. Published by Oxford University Press GigaScience.Supervised machine learning (ML) is used extensively in biology and deserves closer scrutiny. The Data Optimization Model Evaluation (DOME) recommendations aim to enhance the validation and reproducibility of ML research by establishing standards for key aspects such as data handling and processing, optimization, evaluation, and model interpretability. The recommendations help to ensure that key details are reported transparently by providing a structured set of questions. Here, we introduce the DOME registry (URL: registry.dome-ml.org), a database that allows scientists to manage and access comprehensive DOME-related information on published ML studies. The registry uses external resources like ORCID, APICURON, and the Data Stewardship Wizard to streamline the annotation process and ensure comprehensive documentation. By assigning unique identifiers and DOME scores to publications, the registry fosters a standardized evaluation of ML methods. Future plans include continuing to grow the registry through community curation, improving the DOME score definition and encouraging publishers to adopt DOME standards, and promoting transparency and reproducibility of ML in the life sciences.
4.
Piovesan D; Zago D; Joshi P; Kaluza M C D P; Mehdiabadi M; Ramola R; Monzon A M; Reade W; Friedberg I; Radivojac P; Tosatto S C E
CAFA-evaluator: a Python tool for benchmarking ontological classification methods Journal Article
In: Bioinformatics Advances, vol. 4, no. 1, 2024, (Cited by: 4; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:85188993912,
title = {CAFA-evaluator: a Python tool for benchmarking ontological classification methods},
author = {Damiano Piovesan and Davide Zago and Parnal Joshi and M. Clara De Paolis Kaluza and Mahta Mehdiabadi and Rashika Ramola and Alexander Miguel Monzon and Walter Reade and Iddo Friedberg and Predrag Radivojac and Silvio C. E. Tosatto},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-85188993912&origin=inward},
doi = {10.1093/bioadv/vbae043},
year = {2024},
date = {2024-01-01},
journal = {Bioinformatics Advances},
volume = {4},
number = {1},
publisher = {Oxford University Press},
abstract = {© 2024 The Author(s). Published by Oxford University Press.We present CAFA-evaluator, a powerful Python program designed to evaluate the performance of prediction methods on targets with hierarchical concept dependencies. It generalizes multi-label evaluation to modern ontologies where the prediction targets are drawn from a directed acyclic graph and achieves high efficiency by leveraging matrix computation and topological sorting. The program requirements include a small number of standard Python libraries, making CAFA-evaluator easy to maintain. The code replicates the Critical Assessment of protein Function Annotation (CAFA) benchmarking, which evaluates predictions of the consistent subgraphs in Gene Ontology. Owing to its reliability and accuracy, the organizers have selected CAFA-evaluator as the official CAFA evaluation software.},
note = {Cited by: 4; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© 2024 The Author(s). Published by Oxford University Press.We present CAFA-evaluator, a powerful Python program designed to evaluate the performance of prediction methods on targets with hierarchical concept dependencies. It generalizes multi-label evaluation to modern ontologies where the prediction targets are drawn from a directed acyclic graph and achieves high efficiency by leveraging matrix computation and topological sorting. The program requirements include a small number of standard Python libraries, making CAFA-evaluator easy to maintain. The code replicates the Critical Assessment of protein Function Annotation (CAFA) benchmarking, which evaluates predictions of the consistent subgraphs in Gene Ontology. Owing to its reliability and accuracy, the organizers have selected CAFA-evaluator as the official CAFA evaluation software.
5.
Conte A D; Camagni G F; Clementel D; Minervini G; Monzon A M; Ferrari C; Piovesan D; Tosatto S C E
RING 4.0: Faster residue interaction networks with novel interaction types across over 35,000 different chemical structures Journal Article
In: Nucleic Acids Research, vol. 52, no. W1, pp. W306-W312, 2024, (Cited by: 7; Open Access).
Abstract | Altmetric | Dimensions | PlumX | Links:
@article{SCOPUS_ID:85197788039,
title = {RING 4.0: Faster residue interaction networks with novel interaction types across over 35,000 different chemical structures},
author = {Alessio Del Conte and Giorgia F Camagni and Damiano Clementel and Giovanni Minervini and Alexander Miguel Monzon and Carlo Ferrari and Damiano Piovesan and Silvio C. E Tosatto},
url = {https://www.scopus.com/record/display.uri?eid=2-s2.0-85197788039&origin=inward},
doi = {10.1093/nar/gkae337},
year = {2024},
date = {2024-01-01},
journal = {Nucleic Acids Research},
volume = {52},
number = {W1},
pages = {W306-W312},
publisher = {Oxford University Press},
abstract = {© 2024 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.Residue interaction networks (RINs) are a valuable approach for representing contacts in protein structures. RINs have been widely used in various research areas, including the analysis of mutation effects, domain-domain communication, catalytic activity, and molecular dynamics simulations. The RING server is a powerful tool to calculate non-covalent molecular interactions based on geometrical parameters, providing high-quality and reliable results. Here, we introduce RING 4.0, which includes significant enhancements for identifying both covalent and non-covalent bonds in protein structures. It now encompasses seven different interaction types, with the addition of π-hydrogen, halogen bonds and metal ion coordination sites. The definitions of all available bond types have also been refined and RING can now process the complete PDB chemical component dictionary (over 35000 different molecules) which provides atom names and covalent connectivity information for all known ligands. Optimization of the software has improved execution time by an order of magnitude. The RING web server has been redesigned to provide a more engaging and interactive user experience, incorporating new visualization tools. Users can now visualize all types of interactions simultaneously in the structure viewer and network component. The web server, including extensive help and tutorials, is available from URL: https://ring.biocomputingup.it/.},
note = {Cited by: 7; Open Access},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
© 2024 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.Residue interaction networks (RINs) are a valuable approach for representing contacts in protein structures. RINs have been widely used in various research areas, including the analysis of mutation effects, domain-domain communication, catalytic activity, and molecular dynamics simulations. The RING server is a powerful tool to calculate non-covalent molecular interactions based on geometrical parameters, providing high-quality and reliable results. Here, we introduce RING 4.0, which includes significant enhancements for identifying both covalent and non-covalent bonds in protein structures. It now encompasses seven different interaction types, with the addition of π-hydrogen, halogen bonds and metal ion coordination sites. The definitions of all available bond types have also been refined and RING can now process the complete PDB chemical component dictionary (over 35000 different molecules) which provides atom names and covalent connectivity information for all known ligands. Optimization of the software has improved execution time by an order of magnitude. The RING web server has been redesigned to provide a more engaging and interactive user experience, incorporating new visualization tools. Users can now visualize all types of interactions simultaneously in the structure viewer and network component. The web server, including extensive help and tutorials, is available from URL: https://ring.biocomputingup.it/.