A5056593148- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Protein Structure and Dynamics
- Genetics, Bioinformatics, and Biomedical Research
- Machine Learning in Bioinformatics
- Advanced Proteomics Techniques and Applications
- Genetic Neurodegenerative Diseases
- Biomedical and Engineering Education
- RNA Research and Splicing
- Enzyme Structure and Function
- Bioinformatics and Genomic Networks
- Fungal and yeast genetics research
- Scientific Computing and Data Management
- Interdisciplinary Research and Collaboration
- Metabolomics and Mass Spectrometry Studies
- Microbial Metabolic Engineering and Bioproduction
- E-Learning and Knowledge Management
- Protein purification and stability
- Biomedical Text Mining and Ontologies
- Prion Diseases and Protein Misfolding
- Health and Medical Research Impacts
- Wnt/β-catenin signaling in development and cancer
- Connective tissue disorders research
- Cancer Genomics and Diagnostics
- Neurological diseases and metabolism
European Molecular Biology Laboratory
2021-2023
European Molecular Biology Laboratory
2023
University of Padua
2015-2021
Abstract The Pfam database is a widely used resource for classifying protein sequences into families and domains. Since was last described in this journal, over 350 new have been added 33.1 numerous improvements made to existing entries. To facilitate research on COVID-19, we revised the entries that cover SARS-CoV-2 proteome, built regions were not covered by Pfam. We reintroduced Pfam-B which provides an automatically generated supplement contains 136 730 novel clusters of are yet matched...
The last few years have witnessed significant changes in Pfam (https://pfam.xfam.org). number of families has grown substantially to a total 17,929 release 32.0. New additions been coupled with efforts improve existing families, including refinement domain boundaries, their classification into clans, as well functional annotation. We recently began collaborate the RepeatsDB resource definition tandem repeat within Pfam. carried out comparison structural database, namely Evolutionary...
Intrinsically disordered proteins, defying the traditional protein structure-function paradigm, are a challenge to study experimentally. Because large part of our knowledge rests on computational predictions, it is crucial that their accuracy high. The Critical Assessment Intrinsic Disorder prediction (CAID) experiment was established as community-based blind test determine state art in intrinsically regions and subset residues involved binding. A total 43 methods were evaluated dataset 646...
Abstract The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including doubling protein entries, a new disorder ontology, improvements annotation format and completely website. website includes redesigned graphical interface, better search engine, clearer API for programmatic access interface that integrates text mining...
Abstract The MobiDB database (URL: https://mobidb.org/) provides predictions and annotations for intrinsically disordered proteins. Here, we report recent developments implemented in version 4, regarding the format, with novel types of an improved update process. new website includes a re-designed user interface, more effective search engine advanced API programmatic access. schema gives flexibility users, as well simplifying maintenance updates. In addition, entry page visualisation tools...
The MobiDB (URL: mobidb.bio.unipd.it) database of protein disorder and mobility annotations has been significantly updated upgraded since its last major renewal in 2014. Several curated datasets for intrinsic folding upon binding have integrated from specialized databases. indirect evidence also expanded to better capture information available the PDB, such as high temperature residues X-ray structures overall conformational diversity. Novel nuclear magnetic resonance chemical shift data...
Abstract Low complexity regions (LCRs) in protein sequences are characterized by a less diverse amino acid composition compared to typically observed sequence diversity. Recent studies have shown that LCRs may co-occur with intrinsically disordered regions, highly conserved many organisms, and often play important roles functions diseases. In previous decades, several methods been developed identify or bias, but most of them as stand-alone applications currently there is no web-based tool...
The RepeatsDB database (URL: https://repeatsdb.org/) provides annotations and classification for protein tandem repeat structures from the Protein Data Bank (PDB). repeats are ubiquitous in all branches of tree life. accumulation solved new possibilities detection, but also increasing need annotation. Here we present 3.0, which addresses these challenges presents an extended scheme. major conceptual change compared to previous version is hierarchical combining top levels based solely on...
Solubility is an important, albeit not well understood, feature determining protein behavior. It of paramount importance in engineering, where similar folded proteins may behave very different ways solution. Here we present SODA, a novel method to predict the changes solubility based on several physico-chemical properties protein. SODA uses propensity sequence aggregate as intrinsic disorder, plus hydrophobicity and secondary structure preferences estimate solubility. has been trained...
RepeatsDB 2.0 (URL: http://repeatsdb.bio.unipd.it/) is an update of the database annotated tandem repeat protein structures. Repeat proteins are a widespread class non-globular carrying heterogeneous functions involved in several diseases. Here we provide new version with improved classification schema including high quality annotations for ∼5400 features information on start and end positions regions units all entries. The extensive growth unit characterization was possible by applying...
The Feature-Viewer is a lightweight library for the visualization of biological data mapped to protein or nucleotide sequence. It designed ease use while allowing full customization. already used by several resources and allows intuitive visual mapping spectra sequence features different usages.The open source, compatible with state-of-the-art development technologies responsive, also mobile viewing. Documentation usage examples are available online.
Prion-like behavior has been in the spotlight since it was first associated with onset of mammalian neurodegenerative diseases. However, a growing body evidence suggests that this mechanism could be behind regulation processes such as transcription and translation multiple species. Here, we perform stringent computational survey to identify prion-like proteins human proteome. We detected 242 candidate polypeptides computationally assessed their function, protein-protein interaction networks,...
RepeatsDB-lite (http://protein.bio.unipd.it/repeatsdb-lite) is a web server for the prediction of repetitive structural elements and units in tandem repeat (TR) proteins. TRs are widespread but poorly annotated class non-globular proteins carrying heterogeneous functions. extends to all TR types strongly improves performance both terms computational time accuracy over previous methods, with precision above 95% solenoid structures. The algorithm exploits an improved unit library derived from...
ABSTRACT Science, technology, engineering, mathematics, and medicine (STEMM) fields change rapidly are increasingly interdisciplinary. Commonly, STEMM practitioners use short-format training (SFT) such as workshops short courses for upskilling reskilling, but unaddressed challenges limit SFT’s effectiveness inclusiveness. Prior work, including the NSF 2026 Reinventing Scientific Talent proposal, called addressing SFT challenges, a diverse international group of experts in education,...
Science, technology, engineering, mathematics, and medicine (STEMM) fields change rapidly are increasingly interdisciplinary. Commonly, STEMM practitioners use short-format training (SFT) such as workshops short courses for upskilling reskilling, but unaddressed challenges limit SFT's effectiveness inclusiveness. Education researchers, students in SFT courses, organizations have called research strategies that can strengthen terms of effectiveness, inclusiveness, accessibility across...
Collagen V mutations are associated with Elhers–Danlos syndrome (EDS), a group of heritable collagenopathies. structure is not available and the disease‐causing mechanism unclear. To address this issue, we manually curated missense suspected to promote classic type EDS (cEDS) insurgence from literature performed genotype–phenotype correlation study. Further, generated homology model collagen triple helix evaluate pathogenic effects. The resulting was used map known protein–protein...
<ns4:p>Regional Student Groups (RSGs) of the International Society for Computational Biology Council (ISCB-SC) have been instrumental to connect computational biologists globally and create more awareness about bioinformatics education. This article highlights initiatives carried out by RSGs both nationally internationally strengthen present future community. Moreover, we discuss directions organization will take challenges advance further in ISCB-SC main mission: “Nurture new generation...
Despite a fast-growing number of available plant genomes, computational resources are poorly integrated and provide only limited access to the underlying data. Most existing databases focus on DNA/RNA data or specific gene families, with less emphasis protein structure, function variability. In particular, despite economic importance many accessions, there no straightforward ways retrieve visualize information their differences. To fill this gap, we developed PhytoTypeDB...
Abstract Summary Biological data is ever-increasing in amount and complexity. The mapping of this to biological entities such as nucleotide amino acid sequences supports analysis, classification prediction. Sequence alignments comparison allow the transfer knowledge evolutionary-related entities, functional domains, identification binding modification sites. To support these types studies, we developed ProSeqViewer, a tool visualize annotation on single multiple sequence alignments. This...