A5029176853- Protein Structure and Dynamics
- Robotic Path Planning Algorithms
- Computational Fluid Dynamics and Aerodynamics
- Fluid Dynamics and Turbulent Flows
- Gas Dynamics and Kinetic Theory
- Bioinformatics and Genomic Networks
- Machine Learning in Bioinformatics
- Modular Robots and Swarm Intelligence
- Enzyme Structure and Function
- Robotic Mechanisms and Dynamics
- Reinforcement Learning in Robotics
- User Authentication and Security Systems
- Computational Drug Discovery Methods
- Multi-Agent Systems and Negotiation
- RNA and protein synthesis mechanisms
- Genetic Associations and Epidemiology
- Aerodynamics and Fluid Dynamics Research
- Monoclonal and Polyclonal Antibodies Research
- Biometric Identification and Security
- Microbial Metabolic Engineering and Bioproduction
- Advanced Proteomics Techniques and Applications
- Genomics and Rare Diseases
- Protein purification and stability
- Aerospace and Aviation Technology
- Genomics and Phylogenetic Studies
University of Padua
2014-2024
Ospedale di Parma
2017
Forschungszentrum Jülich
2014
COMSATS University Islamabad
2013
Pontifical Catholic University of Peru
2012
Université de Montréal
2007
University of California, Berkeley
2003
Alleanza Contro il Cancro
1999
Polytechnic University of Turin
1964-1997
John Brown University
1997
The authors address the problem of planning optimal grasps. Two general optimality criteria that consider total finger force and maximum are introduced discussed. Their formalization using various metrics on a space generalized forces is detailed. geometric interpretation two leads to an efficient algorithm. An example its use in robotic environment equipped with two-jaw three-jaw described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A major bottleneck in our understanding of the molecular underpinnings life is assignment function to proteins. While experiments provide most reliable annotation proteins, their relatively low throughput and restricted purview have led an increasing role for computational prediction. However, assessing methods protein prediction tracking progress field remain challenging.We conducted second critical assessment functional (CAFA), a timed challenge assess that automatically assign function....
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...
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 Motivation: Intrinsically disordered regions are key for the function of numerous proteins. Due to difficulties in experimental disorder characterization, many computational predictors have been developed with various flavors. Their performance is generally measured on small sets mainly from experimentally solved structures, e.g. Protein Data Bank (PDB) chains. MobiDB has only recently started collect annotations multiple structures. Results: annotates UniProt sequences, allowing us...
The rapid growth of un-annotated missense variants poses challenges requiring novel strategies for their interpretation. From the thermodynamic point view, amino acid changes can lead to a change in internal energy protein and induce structural rearrangements. This is great relevance study diseases design, justifying development prediction methods variant-induced stability changes.Here we propose NeEMO, tool evaluation using an effective representation proteins based on residue interaction...
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....
Antibodies are a class of proteins capable specifically recognizing and binding to virtually infinite number antigens. This malleability makes them the most valuable category biopharmaceuticals for both diagnostic therapeutic applications. The correct identification antigen-binding residues in antibody is crucial all design engineering techniques could also help understand complex antigen mechanisms. However, antibody-binding interface prediction field appears be still rather...
Abstract The Protein Ensemble Database (PED) (URL: https://proteinensemble.org) is the primary resource for depositing structural ensembles of intrinsically disordered proteins. This updated version PED reflects advancements in field, denoting a continual expansion with total 461 entries and 538 ensembles, including those generated without explicit experimental data through novel machine learning (ML) techniques. With this significant increment number few yet-unprecedented new entered...
The dynamics of a gas undergoing nonequilibrium ionization by both radiative (bound-free) and collisional transitions is formulated. Examination the theory leads to number general deductions. rates emission absorption coefficients are all evaluated explicitly from statistical results available for monatomic considered. This makes problem concrete; one also sees that approach other cross sections, transitions, gases would be analogous in most or many respects. It shown spectral complexities...
RepeatsDB (http://repeatsdb.bio.unipd.it/) is a database of annotated tandem repeat protein structures. Tandem repeats pose difficult problem for the analysis structures, as underlying sequence can be highly degenerate. Several types haven been studied over years, but their annotation was done in case-by-case basis, thus making large-scale difficult. We developed to fill this gap. Using state-of-the-art detection methods and manual curation, we systematically Protein Data Bank, predicting 10...
The correct determination of protein–protein interaction interfaces is important for understanding disease mechanisms and rational drug design. To date, several computational methods the prediction protein have been developed, but interface problem still not fully understood. Experimental evidence suggests that location binding sites imprinted in structure, there are major differences among various types: characterising properties can vary a lot depending on type function. selection an...
Abstract 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 Protein Data Bank (PDB) AlphaFoldDB. This latest release features substantial advancements, including annotations over 34 000 unique protein sequences &gt;2000 organisms, representing fifteenfold increase in coverage. Leveraging state-of-the-art structural alignment tools, now offers faster more precise...
Abstract Germline mutations impairing the p16INK4-function have previously been demonstrated to be responsible for genetic predisposition in at least one half of melanoma-prone kindreds North European origin. Familial melanoma also found present an increased risk pancreatic cancer and other cancers, but results relative more common neoplasias incidence, particular, are heterogeneous. We report here a clinical-epidemiological study, including presence additional neoplasias, 14 apparently...
Precision medicine aims to predict a patient's disease risk and best therapeutic options by using that individual's genetic sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is community experiment consisting genotype-phenotype prediction challenges; participants build models, undergo assessment, share key findings. For CAGI 4, three challenges involved exome-sequencing data: Crohn's disease, bipolar disorder, warfarin dosing. Previous included prior versions the...
Abstract Motivation State-of-the-art prediction methods are generating millions of publicly available protein structures. Structured Tandem Repeats Proteins (STRPs) constitute a subclass tandem repeats characterized by repetitive structural motifs. STRPs exhibit distinct propensities for secondary structure and form regular tertiary structures, often comprising large molecular assemblies. They can perform important diverse biological functions due to their highly degenerated sequences, which...
Over the last decade, we have witnessed an incredible growth in amount of available genotype data due to high throughput sequencing (HTS) techniques. This information may be used predict phenotypes medical relevance, and pave way towards personalized medicine. Blood (e.g. ABO Rh) are a purely genetic trait that has been extensively studied for decades, with currently over thirty known blood groups. Given public availability group data, it is interest these from HTS which translate into more...
Abstract Motivation: Repeat proteins form a distinct class of structures where folding is greatly simplified. Several classes have been defined, with solenoid repeats periodicity between ca. 5 and 40 being the most challenging to detect. Such evolve quickly their may be rapidly hidden at sequence level. From structural point view, finding solenoids complicated by presence insertions or multiple domains. To best our knowledge, no automated methods are available characterize from structure....
Von Hippel-Lindau (VHL) syndrome is a hereditary condition predisposing to the development of different cancer forms, related germline inactivation homonymous tumor suppressor pVHL. The best characterized function pVHL ubiquitination dependent degradation Hypoxia Inducible Factor (HIF) via proteasome. It also involved in several cellular pathways acting as molecular hub and interacting with more than 200 proteins. Molecular details plasticity remain large part unknown. Here, we present novel...
The Critical Assessment of Genome Interpretation-5 intellectual disability challenge asked to use computational methods predict patient clinical phenotypes and the causal variant(s) based on an analysis their gene panel sequence data. Sequence data for 74 genes associated with (ID) and/or autism spectrum disorders (ASD) from a cohort 150 patients range neurodevelopmental manifestations (i.e. ID, autism, epilepsy, microcephaly, macrocephaly, hypotonia, ataxia) have been made available this...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT17-Hydroxypregnanes from Androstane CompoundsPietro de Ruggieri and Carlo FerrariCite this: J. Am. Chem. Soc. 1959, 81, 21, 5725–5727Publication Date (Print):November 1, 1959Publication History Published online1 May 2002Published inissue 1 November 1959https://pubs.acs.org/doi/10.1021/ja01530a048https://doi.org/10.1021/ja01530a048research-articleACS PublicationsRequest reuse permissionsArticle Views147Altmetric-Citations13LEARN ABOUT THESE...