A5014042889- Protein Structure and Dynamics
- Scientific Computing and Data Management
- Research Data Management Practices
- Enzyme Structure and Function
- Bioinformatics and Genomic Networks
- Nanoparticles: synthesis and applications
- Invertebrate Immune Response Mechanisms
- Advanced Proteomics Techniques and Applications
- Biomedical Text Mining and Ontologies
- Neurobiology and Insect Physiology Research
- Heavy Metals in Plants
- Microbial Metabolic Engineering and Bioproduction
- Biological Activity of Diterpenoids and Biflavonoids
- Cancer therapeutics and mechanisms
- Wound Healing and Treatments
- Genetics, Bioinformatics, and Biomedical Research
- Ion channel regulation and function
- Metabolomics and Mass Spectrometry Studies
- Metal complexes synthesis and properties
- Plant Gene Expression Analysis
- Marine Ecology and Invasive Species
- Machine Learning in Bioinformatics
- Hydraulic flow and structures
- Graphene and Nanomaterials Applications
- Forensic Fingerprint Detection Methods
University of Padua
2013-2024
Veneto Nanotech (Italy)
2013-2017
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...
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora databases tools deployed, technically complex diverse implementations, across spectrum disciplines. The corpus documentation resources is fragmented Web, with much redundancy, has lacked common standard information. outcome scientists must often struggle find, understand, compare use best for...
Leucine-rich repeat kinase 1 and 2 (LRRK1 LRRK2) are large multidomain proteins containing kinase, GTPase multiple protein-protein interaction domains, but only mutations in LRRK2 linked to familial Parkinson's disease (PD). Independent studies suggest that exists the cell as a complex compatible with size of dimer. However, whether this is truly homodimer or heterologous formed by monomeric other has not been definitively proven due limitations obtaining highly pure suitable for structural...
We have applied different analytical techniques for studying the size and metal composition of nanoparticles (NPs) microparticles in tattoo inks. The morphology distribution particles were determined by transmission electron microscopy (TEM) dynamic light scattering (DLS). These allowed us to obtain information on all mixtures. Higher resolution characterization distributions was achieved means asymmetric flow field fractionation (AF4) combined with multi-angle (MALS) detection, which...
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...
Snake pre-synaptic neurotoxins endowed with phospholipase A(2) activity are potent inducers of paralysis through the specific disruption neuromuscular junction membrane and represent a valuable tool for investigating neuronal degeneration recovery. They have different structural complexity wide range lethal potency enzymatic activity, although they share similar mechanism action. Although no correlation has been reported between neurotoxicity toxicity increases oligomers show 10-fold lower...
Nowadays scientists massively produce diverse datasets in many communities. They need to combine them answer scientific or novel questions. To do so, these computational resources first be found by search engines. Bioschemas provides a simple and lightweight mechanism annotate online standardized way expose key metadata. improve the accessibility value of existing emerging communities, we aim develop an automated system assess adoption Bioschemas, work with identified groups that have...
Octopus vulgaris hemocyanin shows a particular self-assembling pattern, characterized by hierarchical organization of monomers. The highest molecular weight aggregate is decamer, the stability which in solution depends on several parameters. Different pH values, buffer compositions, H₂O/D₂O ratios and Hofmeister's salts result modifications aggregation state hemocyanin. new QUAFIT method, recently applied to derive structure decameric monomeric assembly from small-angle scattering data, used...
One of the goals ELIXIR Intrinsically Disordered Protein (IDP) community is create a registry called IDPcentral. The will aggregate data contained in community's specialist sources such as DisProt, MobiDB, and Ensemble Database (PED) so that proteins are known to be intrinsically disordered can discovered; with summary details protein presented, source consulted for more detailed data. At BioHackathon-Europe 2020, we aimed investigate feasibility populating IDPcentral harvesting Bioschemas...
Hemocyanin (Hc) is an oxygen carrier protein in which binding regulated by allosteric effectors such as H(+) and L-lactate. Isothermal titration calorimetric measurements showed that L-lactate binds to dodecameric heterohexameric Hc the CaeSS3 homohexamer but not CaeSS2 monomer. The of lactate caused no change optical absorption x-ray spectra either oxy- or deoxy-Hc, suggesting structural rearrangement active site occurred. At pH 6.5, rate constant k(obs) obtained flash photolysis a...
Increasingly large numbers of proteins require methods for functional annotation. This is typically based on pairwise inference from the homology either protein sequence or structure. Recently, similarity networks have been presented to leverage both ability visualize relationships between and assess transferability inference. Here we present PANADA, a novel toolkit visualization analysis in Cytoscape. Networks can be constructed structural alignments set or, alternatively, by database...
First observation of AgNPs dynamics in the wounds real patients through elemental imaging and speciation.
The document presents how a workshop for the local Italian ELIXIR community steered an improvement of quality and adoption Bioschemas, series semantic annotation templates tools, data samples developed by Interoperability platform. Gathering small number different end-users having them focus on applying Bioschemas specification to their tools resulted in recruitment early adopters, eight annotated resources, examples future users more than ten suggestions improvement. This approach could be...