arXiv subjects

Damiano Piovesan

Publications and source records attributed to Damiano Piovesan.

4 recordsLinked to original sources

arXiv2025

Towards a Unified Framework for Determining Conformational Ensembles of Disordered Proteins

Disordered proteins play essential roles in myriad cellular processes, yet their structural characterization remains a major challenge due to their dynamic and heterogeneous nature. We here present a community-driven initiative to address this problem by advocating a unified framework for determining conformational ensembles of disordered proteins. Our aim is to integrate state-of-the-art experimental techniques with advanced computational methods, including knowledge-based sampling, enhanced molecular dynamics, and machine learning models. The modular framework comprises three interconnected components: experimental data acquisition, computational ensemble generation, and validation. The systematic development of this framework will ensure the accurate and reproducible determination of conformational ensembles of disordered proteins. We highlight the open challenges necessary to achieve this goal, including force field accuracy, efficient sampling, and environmental dependency, advocating for collaborative benchmarking and standardized protocols.

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arXiv2024

DOME Registry: Implementing community-wide recommendations for reporting supervised machine learning in biology

Supervised machine learning (ML) is used extensively in biology and deserves closer scrutiny. The 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, promoting transparency and reproducibility of ML in the life sciences.

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arXiv2024

CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods

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.

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arXiv2023

Best practices for the manual curation of Intrinsically Disordered Proteins in DisProt

The DisProt database is a significant resource containing manually curated data on experimentally validated intrinsically disordered proteins (IDPs) and regions (IDRs) from the literature. Developed in 2005, its primary goal was to collect structural and functional information into proteins that lack a fixed three-dimensional (3D) structure. Today, DisProt has evolved into a major repository that not only collects experimental data but also contributes significantly to our understanding of the IDPs/IDRs roles in various biological processes, such as autophagy or the life cycle mechanisms in viruses, or their involvement in diseases (such as cancer and neurodevelopmental disorders). DisProt offers detailed information on the structural states of IDPs/IDRs, including state transitions, interactions, and their functions, all provided as curated annotations. One of the central activities of DisProt is the meticulous curation of experimental data from the literature. For this reason, to ensure that every expert and volunteer curator possesses the requisite knowledge for data evaluation, collection, and integration, training courses and curation materials are available. However, biocuration guidelines concur on the importance of developing robust guidelines that not only provide critical information about data consistency but also ensure data acquisition.This guideline aims to provide both biocurators and external users with best practices for manually curating IDPs and IDRs in DisProt. It describes every step of the literature curation process and provides use cases of IDP curation within DisProt. Database URL: https://disprot.org/

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