A5066560665- Protein Structure and Dynamics
- Enzyme Structure and Function
- Bioinformatics and Genomic Networks
- RNA and protein synthesis mechanisms
- Machine Learning in Bioinformatics
- Genomics and Phylogenetic Studies
- Cancer, Hypoxia, and Metabolism
- Advanced Proteomics Techniques and Applications
- Computational Drug Discovery Methods
- Microbial Metabolic Engineering and Bioproduction
- Mitochondrial Function and Pathology
- Genomics and Rare Diseases
- Genetics, Bioinformatics, and Biomedical Research
- ATP Synthase and ATPases Research
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Metabolomics and Mass Spectrometry Studies
- Fibroblast Growth Factor Research
- Genetics and Neurodevelopmental Disorders
- Genetic Neurodegenerative Diseases
- RNA modifications and cancer
- Biomedical Text Mining and Ontologies
- Cellular transport and secretion
- Cardiomyopathy and Myosin Studies
- Mass Spectrometry Techniques and Applications
Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies
2024-2025
National Research Council
2018-2025
University of Padua
2015-2024
Universidade de São Paulo
2024
National Academies of Sciences, Engineering, and Medicine
2024
Neuroscience Institute
2015-2023
University College London
2018-2023
SIB Swiss Institute of Bioinformatics
2023
Stanford University
2023
Phoenix Bioinformatics
2023
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...
The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains conserved sites. InterProScan is the underlying software that allows nucleic acid to be searched against InterPro's signatures. Signatures are predictive models which describe or sites, provided by multiple databases. combines signatures representing equivalent additional information such as descriptions, literature...
Abstract The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains conserved sites. Here, we report recent developments with (version 90.0) its associated software, including updates to data content the website. These extend enrich information provided by InterPro, provide a more user friendly access data. Additionally, have worked on adding Pfam website features website, as...
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...
The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains sites. Here, we report recent developments with (version 70.0) its associated software, including an 18% growth in size terms on new entries, updates to content, inclusion additional entry type, refined modelling discontinuous domains, development a programmatic interface website. These extend enrich information provided by InterPro,...
Abstract In protein structure prediction, a considerable number of alternative models are usually produced from which subsequently the final model has to be selected. Thus, scoring function for identification best within an ensemble is key component most prediction pipelines. QMEAN, stands Qualitative Model Energy ANalysis, composite describing major geometrical aspects structures. Five different structural descriptors used. The local geometry analyzed by new kind torsion angle potential...
Abstract Motivation: Intrinsically disordered regions are key for the function of numerous proteins, and scant available experimental annotations suggest existence different disorder flavors. While efficient predictions required to annotate entire genomes, most existing methods require sequence profiles prediction, making them cumbersome high-throughput applications. Results: In this work, we present an ensemble protein predictors called ESpritz. These based on bidirectional recursive neural...
The formation of amyloid aggregates upon protein misfolding is related to several devastating degenerative diseases. propensities different sequences aggregate into amyloids, how they are enhanced by pathogenic mutations, the presence aggregation hot spots stabilizing pathological interactions, establishing cross-amyloid interactions between co-aggregating proteins, all rely at molecular level on stability cross-beta structure. Our redesigned server, PASTA 2.0, provides a versatile platform...
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...
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...
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...
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...
MobiDB (http://mobidb.bio.unipd.it/) is a database of intrinsically disordered and mobile proteins. Intrinsically regions are key for the function numerous Here we provide new version MobiDB, centralized source aimed at providing most complete picture on different flavors disorder in protein structures covering all UniProt sequences (currently over 80 million). The features three levels annotation: manually curated, indirect predicted. Manually curated data extracted from DisProt database....
Membraneless organelles (MOs) are dynamic liquid condensates that host a variety of specific cellular processes, such as ribosome biogenesis or RNA degradation. MOs form through liquid-liquid phase separation (LLPS), process relies on multivalent weak interactions the constituent proteins and other macromolecules. Since first discoveries certain being able to drive LLPS, it emerged general mechanism for effective organization space is exploited in all kingdoms life. While numerous...
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.