Explanipedia

AlphaFlex: Ensembles of the human proteome representing disordered regions Open

Zi Hao Liu, Oufan Zhang, Kunyang Sun, Nicolas L. Fawzi, Silvio C. E. Tosatto , et al. · 2025

Over a third of residues in the canonical human proteome are predicted to fall within intrinsically disordered protein regions (IDRs), which do not adopt stable folded structures. These IDRs play critical roles in biological regulation and…

Integrative Multi-Omics Characterization and Structural Insights into the Poorly Annotated Integrin ITGA6 X1X2 Isoform in Mammals Open

Ximena Aixa Castro Naser, Alessandro Cestaro, Silvio C. E. Tosatto, Emanuela Leonardi · 2025

Background: Accurate annotation of gene isoforms remains one of the major obstacles in translating genomic data into meaningful biological insight. Laminin-binding integrins, particularly integrin α6 (ITGA6), exemplify this challenge throu…

Mathematical modeling and simulation of tumor-induced angiogenesis in retinal hemangioblastoma Open

Franco Pradelli, Giovanni Minervini, Pradeep Venkatesh, Shorya Vardhan Azad, Héctor Gómez , et al. · 2025

Retinal Hemangioblastoma (RH) is the most frequent manifestation of the von Hippel-Lindau syndrome (VHL), a rare disease associated with the germline mutation of the von Hippel-Lindau protein (pVHL). An emblematic feature of RH is the high…

Decoding protein structures with residue interaction networks Open

Sol C Begue, Emanuela Leonardi, Silvio C. E. Tosatto · 2025

The rise of AlphaFold and similar structure predictors has made it possible to determine the 3D structure of almost any protein from its amino acid sequence. Residue interaction networks (RINs), graphs where residues are represented as nod…

Critical Assessment of Protein Intrinsic Disorder Round 3 ‐ Predicting Disorder in the Era of Protein Language Models Open

Mahta Mehdiabadi, Alessio Del Conte, María Victoria Nugnes, Maria Cristina Aspromonte, Silvio C. E. Tosatto , et al. · 2025

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…

GeomeTRe: accurate calculation of geometrical descriptors of tandem repeat proteins Open

Zarifa Osmanli, Enza Ferrero, Alexander Miguel Monzón, Silvio C. E. Tosatto, Damiano Piovesan · 2025

Motivation Structured tandem repeat proteins (STRPs) are characterized by preserved structural motifs arranged in a modular way. The structural and functional diversity of STRPs makes them particularly important for studying evolution and …

ngx-mol-viewers: Angular components for interactive molecular visualization in bioinformatics Open

Damiano Clementel, Alessio Del Conte, Alexander Miguel Monzón, Silvio C. E. Tosatto · 2025

Advancements in bioinformatics have been propelled by technologies like machine learning and have resulted in substantial increases in data generated from both empirical observations and computational models. Hence, well-known biological d…

Open and Sustainable AI: challenges, opportunities and the road ahead in the life sciences (October 2025 -- Version 2) Open

Gavin Farrell, Eleni Adamidi, Rafael Andrade Buono, Mihail Anton, Omar Abdelghani Attafi , et al. · 2025

Artificial intelligence (AI) has recently seen transformative breakthroughs in the life sciences, expanding possibilities for researchers to interpret biological information at an unprecedented capacity, with novel applications and advance…

MobiDB-lite 4.0: faster prediction of intrinsic protein disorder and structural compactness Open

Mahta Mehdiabadi, Matthias Blum, Giulio Tesei, Sören von Bülow, Kresten Lindorff‐Larsen , et al. · 2025

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 …

GeomeTRe: accurate calculation of geometrical descriptors of tandem repeat proteins Open

Zarifa Osmanli, Enza Ferrero, Alexander Miguel Monzón, Silvio C. E. Tosatto, Damiano Piovesan · 2025

Structured tandem repeat proteins (STRPs) are characterized by preserved structural motifs arranged in a modular way. The structural and functional diversity of STRPs makes them particularly important for studying evolution, novel structur…

Towards a Unified Framework for Determining Conformational Ensembles of Disordered Proteins Open

Maria Cristina Aspromonte, Michael Feig, Kresten Lindorff‐Larsen, Frans A. A. Mulder, Péter Nagy , et al. · 2025

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 …

Genetic variants and phenotypic data curated for the CAGI6 intellectual disability panel challenge Open

Maria Cristina Aspromonte, Alessio Del Conte, Roberta Polli, Demetrio Baldo, Francesco Benedicenti , et al. · 2025

Neurodevelopmental disorders (NDDs) are common conditions including clinically diverse and genetically heterogeneous diseases, such as intellectual disability, autism spectrum disorders, and epilepsy. The intricate genetic underpinnings of…

Mathematical Modeling and Simulation of Tumor-Induced Angiogenesis in Retinal Hemangioblastoma Open

Franco Pradelli, Giovanni Minervini, Pradeep Venkatesh, Shorya Vardhan Azad, Héctor Gómez , et al. · 2025

Retinal Hemangioblastoma (RH) is the most frequent manifestation of the von Hippel-Lindau syndrome (VHL), a rare disease associated with the germline mutation of the von Hippel-Lindau protein (pVHL). An emblematic feature of RH is the high…

CAGI6 ID panel challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (NDDs) Open

Maria Cristina Aspromonte, Alessio Del Conte, Shaowen Zhu, Wuwei Tan, Yang Shen , et al. · 2025

The Genetics of Neurodevelopmental Disorders Lab in Padua provided a new intellectual disability (ID) Panel challenge for computational methods to predict patient phenotypes and their causal variants in the context of the Critical Assessme…

APICURON: Database for crediting & recognition of biocuration activities Open

Federica Quaglia, Silvio C. E. Tosatto · 2025

DRMAAtic: dramatically improve your cluster potential Open

Alessio Del Conte, Hamidreza Ghafouri, Damiano Clementel, Ivan Mičetić, Damiano Piovesan , et al. · 2024

Motivation The accessibility and usability of high-performance computing (HPC) resources remain significant challenges in bioinformatics, particularly for researchers lacking extensive technical expertise. While Distributed Resource Manage…

Searching and Using MobiDB Resource 6 to Explore Predictions and Annotations for Intrinsically Disordered Proteins Open

Maria Cristina Aspromonte, Federica Quaglia, Alexander Miguel Monzón, Damiano Clementel, Alessio Del Conte , et al. · 2024

Intrinsically disordered proteins (IDPs) make up around 30% of eukaryotic proteomes and play a crucial role in cellular processes and in pathological conditions such as neurodegenerative disorders and cancers. However, IDPs exhibit dynamic…

InterPro: the protein sequence classification resource in 2025 Open

Matthias Blum, Antonina Andreeva, Laise Cavalcanti Florentino, Sara Chuguransky, Tiago Grego , et al. · 2024

InterPro (https://www.ebi.ac.uk/interpro) is a freely accessible resource for the classification of protein sequences into families. It integrates predictive models, known as signatures, from multiple member databases to classify sequences…

The Pfam protein families database: embracing AI/ML Open

Typhaine Paysan‐Lafosse, Antonina Andreeva, Matthias Blum, Sara Chuguransky, Tiago Grego , et al. · 2024

The Pfam protein families database is a comprehensive collection of protein domains and families used for genome annotation and protein structure and function analysis (https://www.ebi.ac.uk/interpro/). This update describes major developm…

STRPsearch: fast detection of structured tandem repeat proteins Open

Soroush Mozaffari, Paula Nazarena Arrías, Damiano Clementel, Damiano Piovesan, Carlo Ferrari , et al. · 2024

Motivation Structured Tandem Repeats Proteins (STRPs) constitute a subclass of tandem repeats characterized by repetitive structural motifs. These proteins exhibit distinct secondary structures that form repetitive tertiary arrangements, o…

RepeatsDB in 2025: expanding annotations of structured tandem repeats proteins on AlphaFoldDB Open

Damiano Clementel, Paula Nazarena Arrías, Soroush Mozaffari, Zarifa Osmanli, Ximena Aixa Castro , et al. · 2024

RepeatsDB (URL: https://repeatsdb.org) stands as a key resource for the classification and annotation of Structured Tandem Repeat Proteins (STRPs), incorporating data from both the Protein Data Bank (PDB) and AlphaFoldDB. This latest relea…

MOBIDB in 2025: integrating ensemble properties and function annotations for intrinsically disordered proteins Open

Damiano Piovesan, Alessio Del Conte, Mahta Mehdiabadi, Maria Cristina Aspromonte, Matthias Blum , et al. · 2024

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 se…

Diversity and structural‐functional insights of alpha‐solenoid proteins Open

Paula Nazarena Arrías, Zarifa Osmanli, E G Peralta, Patricio Chinestrad, Alexander Miguel Monzón , et al. · 2024

Alpha‐solenoids are a significant and diverse subset of structured tandem repeat proteins (STRPs) that are important in various domains of life. This review examines their structural and functional diversity and highlights their role in cr…

Genetic Variants and Phenotypic Data Curated for the CAGI6 Intellectual Disability Panel Challenge Open

Maria Cristina Aspromonte, Alessio Del Conte, Roberta Polli, Demetrio Baldo, Francesco Benedicenti , et al. · 2024

Neurodevelopmental disorders (NDDs) are common conditions including clinically diverse and genetically heterogeneous diseases, such as intellectual disability, autism spectrum disorders, and epilepsy. The intricate genetic underpinnings of…

8485 Transcriptome Profiling Of Pediatric Adrenocortical Tumors (pACT) According To Disease Presentation Reinforces Prognostic Markers And Reveals A Lincrna As A Potential Therapeutic Target Open

A B Arruda, R P da Silva-Júnior, Mônica Freire Stecchini, Junier Marrero-Gutiérrez, Izilda Aparecida Cardinalli , et al. · 2024

Disclosure: A.B. Arruda: None. R.P. da Silva-Júnior: None. M.F. Stecchini: None. J. Marrero-Gutiérrez: None. I. Cardinalli: None. T. Junqueira: None. C. Scrideli: None. C.A. Molina: None. T. Silvio: None. T. Silvio: None. F. Coeli-Lacchini…

In Silico Exploration of AHR-HIF Pathway Interplay: Implications for Therapeutic Targeting in ccRCC Open

Francesco Gregoris, Giovanni Minervini, Silvio C. E. Tosatto · 2024

The oxygen-sensing pathway is a crucial regulatory circuit that defines cellular conditions and is extensively exploited in cancer development. Pathogenic mutations in the von Hippel–Lindau (VHL) tumour suppressor impair its role as a mast…

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

Omar Abdelghani Attafi, Damiano Clementel, Konstantinos Kyritsis, Emidio Capriotti, Gavin Farrell , et al. · 2024

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 …

STRPsearch: fast detection of structured tandem repeat proteins Open

Soroush Mozaffari, Paula Nazarena Arrías, Damiano Clementel, Damiano Piovesan, Carlo Ferrari , et al. · 2024

Motivation State-of-the-art prediction methods are generating millions of publicly available protein structures. Structured Tandem Repeats Proteins (STRPs) constitute a subclass of tandem repeats characterized by repetitive structural moti…

RING 4.0: faster residue interaction networks with novel interaction types across over 35,000 different chemical structures Open

Alessio Del Conte, Giorgia F Camagni, Damiano Clementel, Giovanni Minervini, Alexander Miguel Monzón , et al. · 2024

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, cat…

A PDZ scaffolding/CaM‐mediated pathway in Cryptochrome signaling Open

Massimo Bellanda, Milena Damulewicz, Barbara Zambelli, Elisa Costanzi, Francesco Gregoris , et al. · 2024

Cryptochromes are cardinal constituents of the circadian clock, which orchestrates daily physiological rhythms in living organisms. A growing body of evidence points to their participation in pathways that have not traditionally been assoc…

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