A5060625212- Protein Structure and Dynamics
- Glycosylation and Glycoproteins Research
- Enzyme Structure and Function
- Viral Infectious Diseases and Gene Expression in Insects
- Monoclonal and Polyclonal Antibodies Research
- Machine Learning in Bioinformatics
- Genomics and Phylogenetic Studies
- Protein purification and stability
- Bioinformatics and Genomic Networks
- Carbohydrate Chemistry and Synthesis
- Genetics, Bioinformatics, and Biomedical Research
- Mass Spectrometry Techniques and Applications
- Computational Drug Discovery Methods
- RNA and protein synthesis mechanisms
- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Microbial Metabolic Engineering and Bioproduction
- Machine Learning in Materials Science
- Polyamine Metabolism and Applications
- Identification and Quantification in Food
- Analytical Chemistry and Chromatography
- Cell Image Analysis Techniques
- Probiotics and Fermented Foods
- Pharmacological Effects and Assays
- Gene expression and cancer classification
Bioprocessing Technology Institute
2016-2025
Agency for Science, Technology and Research
2016-2025
Star Technology and Research (United States)
2023
University of Manchester
2020
University of Padua
2010-2017
National Institute for Bioprocessing Research and Training
2016
New England Biolabs (United States)
2016
Forschungszentrum Jülich
2014
COMSATS University Islamabad
2013
Istituto Nazionale Biostrutture e Biosistemi
2012
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...
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...
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....
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...
Abstract Motivation: Disordered protein regions are key to the function of numerous processes within an organism and determination a protein's biological role. The most common source for disorder annotations, DisProt, covers only fraction available sequences. Alternatively, Protein Data Bank (PDB) has been mined missing residues in X-ray crystallographic structures. Herein, we provide centralized data on different flavours structures, MobiDB, building expanding content provided by already...
Abstract Motivation: Residue interaction networks (RINs) have been used in the literature to describe protein 3D structure as a graph where nodes represent residues and edges physico–chemical interactions, e.g. hydrogen bonds or van-der-Waals contacts. Topological network parameters can be calculated over RINs correlated with various aspects of function. Here we present novel web server, RING, construct physico–chemically valid interactively from PDB files for subsequent visualization...
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...
CSpritz is a web server for the prediction of intrinsic protein disorder. It combination previous Spritz with two novel orthogonal systems developed by our group (Punch and ESpritz). Punch based on sequence structural templates trained support vector machines. ESpritz an efficient single method bidirectional recursive neural networks. was extended to filter predictions homologues. After extensive testing, are combined averaging their probabilities. The website can elaborate or multiple...
Abstract Motivation: Electrostatic calculations are an important tool for deciphering many functional mechanisms in proteins. Generalized Born (GB) models offer a fast and convenient computational approximation over other implicit solvent-based electrostatic models. Here we present novel GB-based web server, using the program Bluues, to calculate numerous features including pKa-values surface potentials. The output is organized allowing both experts beginners rapidly sift data. A feature of...
Abstract Motivation The behavior of a protein is encoded in its sequence, which can be used to predict distinct features such as secondary structure, intrinsic disorder or amphipathicity. Integrating these and other help explain the context-dependent proteins. However, most tools focus on single aspect, hampering holistic understanding structure. Here, we present Fast Estimator Latent Local Structure (FELLS) visualize structural from sequence. FELLS provides disorder, aggregation low...
GlycoStore is a curated chromatographic, electrophoretic and mass-spectrometry composition database of N-, O-, glycosphingolipid (GSL) glycans free oligosaccharides associated with range glycoproteins, glycolipids biotherapeutics. The built on publicly available experimental datasets from GlycoBase developed in the Oxford Glycobiology Institute then National for Bioprocessing Research Training (NIBRT). It has now been extended to include recently published in-house data collections...
Aberrant glycosylation has been associated with a number of diseases including cancer. Our aim was to elucidate changes in whole plasma N-glycosylation between colorectal cancer (CRC) cases and controls one the largest cohorts its kind. A set 633 CRC patients 478 age gender matched analysed. Additionally, were stratified into four stages. Moreover, N-glycan analysis carried out 40 collected prior initial diagnosis CRC. Statistically significant differences observed N-glycome at all stages...
Abstract Background We describe Distill, a suite of servers for the prediction protein structural features: secondary structure; relative solvent accessibility; contact density; backbone motifs; residue maps at 6, 8 and 12 Angstrom; coarse topology. The are based on large-scale ensembles recursive neural networks trained large, up-to-date, non-redundant subsets Protein Data Bank. Together with feature predictions, Distill includes server C α traces short proteins (up to 200 amino acids)....
Abstract Background Protein topology representations such as residue contact maps are an important intermediate step towards ab initio prediction of protein structure. Although improvements have occurred over the last years, problem accurately predicting from primary sequences is still largely unsolved. Among reasons for this unbalanced nature (with far fewer examples contacts than non-contacts), formidable challenge capturing long-range interactions in maps, intrinsic difficulty mapping...
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...
Protein inter-residue contact maps provide a translation and rotation invariant topological representation of protein. They can be used as an intermediary step in protein structure predictions. However, the prediction represents unbalanced problem far fewer examples contacts than non-contacts exist structure. In this study we explore possibility completely eliminating nature map by predicting real-value distances between residues. Predicting full distance applying them predictions has been...
High-throughput glycan analysis has become an important part of biopharmaceutical production and quality control. However, it is still a significant challenge in the field glycomics to easily deduce isomeric structures, especially high-throughput manner. Ion mobility spectrometry (IMS) excellent tool for differentiating structures. demonstrations utility IMS workflows such as liquid chromatography-fluorescence-mass (LC-FLR-MS) have been limited with only small amount collision cross section...
Abstract Background Prediction of protein structures from their sequences is still one the open grand challenges computational biology. Some approaches to structure prediction, especially ab initio ones, rely some extent on prediction residue contact maps. Residue map predictions have been assessed at CASP competition for several years now. Although it has shown that exact maps generally yield correct three-dimensional structures, this true only a relatively low resolution (3–4 Å native...