Damiano Piovesan
A5000882827- Protein Structure and Dynamics
- Bioinformatics and Genomic Networks
- Machine Learning in Bioinformatics
- Enzyme Structure and Function
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Advanced Proteomics Techniques and Applications
- Microbial Metabolic Engineering and Bioproduction
- Computational Drug Discovery Methods
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Rare Diseases
- Scientific Computing and Data Management
- RNA Research and Splicing
- Biomedical Text Mining and Ontologies
- Mass Spectrometry Techniques and Applications
- Genetics and Neurodevelopmental Disorders
- Cancer, Hypoxia, and Metabolism
- Bacteriophages and microbial interactions
- Fibroblast Growth Factor Research
- Epigenetics and DNA Methylation
- Cell Image Analysis Techniques
- Metabolomics and Mass Spectrometry Studies
- Genetic Neurodegenerative Diseases
- Genomic variations and chromosomal abnormalities
- Biofuel production and bioconversion
University of Padua
2016-2025
University of Bologna
2009-2013
COMSATS University Islamabad
2013
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...
InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and predict the presence of important domains sites. InterProScan underlying software that allows both nucleic acid be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with associated software, including addition two new databases (SFLD CDD), functionality include residue-level annotation...
Automated annotation of protein function is challenging. As the number sequenced genomes rapidly grows, overwhelming majority products can only be annotated computationally. If computational predictions are to relied upon, it crucial that accuracy these methods high. Here we report results from first large-scale community-based critical assessment (CAFA) experiment. Fifty-four representing state art for prediction were evaluated on a target set 866 proteins 11 organisms. Two findings stand...
Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes residues and arcs physico–chemical interactions. RINs have been extensively successfully used for analysing mutation effects, folding, domain–domain communication catalytic activity. Here we present RING 2.0, a new version the software identification covalent non-covalent bonds in structures, including π–π stacking π–cation 2.0 is extremely fast generates both intra inter-chain...
The Database of Protein Disorder (DisProt, URL: www.disprot.org) has been significantly updated and upgraded since its last major renewal in 2007. current release holds information on more than 800 entries IDPs/IDRs, i.e. intrinsically disordered proteins or regions that exist function without a well-defined three-dimensional structure. We have re-curated previous to purge DisProt from conflicting cases, also the functional classification scheme reflect continuous advance field past 10 years...
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 Motivation Intrinsic disorder (ID) is established as an important feature of protein sequences. Its use in proteome annotation however hampered by the availability many methods with similar performance at single residue level, which have mostly not been optimized to predict long ID regions size comparable domains. Results Here, we focused on providing a consensus-based prediction, MobiDB-lite, for highly specific (i.e. few false positive) predictions disorder. The method uses eight...
Abstract The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository manually curated annotations intrinsically disordered proteins and regions from literature. We report here recent updates DisProt version 9, including a restyled web interface, refactored Ontology (IDPO), improvements in curation process significant content growth around 30%. Higher quality consistency provided by newly implemented reviewing training curators. increased...
Abstract Residue interaction networks (RINs) are used to represent residue contacts in protein structures. Thanks the advances network theory, RINs have been proved effective as an alternative coordinate data analysis of complex systems. The RING server calculates high quality and reliable non-covalent molecular interactions based on geometrical parameters. Here, we present new 3.0 version extending previous functionality several ways. underlying software library has re-engineered improve...
Abstract The MobiDB database (URL: https://mobidb.org/) is a knowledge base of intrinsically disordered proteins. aggregates disorder annotations derived from the literature and experimental evidence along with predictions for all known protein sequences. generates new captures functional significance regions by processing combining complementary sources information. Since its first release 10 years ago, has evolved in order to improve quality coverage accessibility. now reached maturity...
Abstract Intrinsically disordered regions (IDRs) defying the traditional protein structure–function paradigm have been difficult to analyze. The availability of accurate structure predictions on a large scale in AlphaFoldDB offers fresh perspective IDR prediction. Here, we establish three baselines for prediction from models based recent CAID dataset. Surprisingly, is highly competitive predicting both IDRs and conditionally folded binding regions, demonstrating plasticity disorder continuum.
Abstract DisProt (URL: https://disprot.org) is the gold standard database for intrinsically disordered proteins and regions, providing valuable information about their functions. The latest version of brings significant advancements, including a broader representation functions an enhanced curation process. These improvements aim to increase both quality annotations coverage at sequence level. Higher has been achieved by adopting additional evidence codes. Quality improved systematically...
Protein intrinsic disorder (ID) is a complex and context-dependent phenomenon that covers continuum between fully disordered states folded with long dynamic regions. The lack of ground truth fits all ID flavors the potential for order-to-disorder transitions depending on specific conditions makes prediction challenging. CAID2 challenge aimed to evaluate performance different methods across benchmarks, leveraging annotation provided by DisProt database, which stores coordinates regions when...
Abstract Residue interaction networks (RINs) are a valuable approach for representing contacts in protein structures. RINs have been widely used various research areas, including the analysis of mutation effects, domain-domain communication, catalytic activity, and molecular dynamics simulations. The RING server is powerful tool to calculate non-covalent interactions based on geometrical parameters, providing high-quality reliable results. Here, we introduce 4.0, which includes significant...
Abstract 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 families and predict presence domains significant sites. The database provides annotations over 200 million sequences, ensuring extensive coverage UniProtKB, standard repository includes mappings several other major resources, such Gene Ontology (GO),...
Abstract The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. new version, PED 4.0, completely redesigned reimplemented with cutting-edge technology now about six times more data (162 versus 24 entries 242 60 ensembles) a broader representation state the art ensemble generation methods than previous version. database renewed...
Identifying protein functions can be useful for numerous applications in biology. The prediction of gene ontology (GO) functional terms from sequence remains however a challenging task, as shown by the recent CAFA experiments. Here we present INGA, web server developed to predict function combination three orthogonal approaches. Sequence similarity and domain architecture searches are combined with protein-protein interaction network data derive consensus predictions GO using enrichment....
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 earlier version of MobiDB-lite is currently used in large-scale proteome annotation platforms to detect intrinsic disorder. However, new theoretical models allow for the classification intrinsically disordered regions into subtypes from sequence features associated with specific polymeric properties or compositional bias.MobiDB-lite 3.0 maintains its previous speed and performance but also provides a finer disorder by identifying characteristics polyolyampholytes, positive negative...
The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the (PDB). goal of PDBe-KB place macromolecular structure their biological context by developing standardised exchange formats integrating partner into a knowledge graph that can provide valuable insights. Since we described 2019, there have been significant...