A5057595671- Protein Structure and Dynamics
- SARS-CoV-2 and COVID-19 Research
- Monoclonal and Polyclonal Antibodies Research
- RNA and protein synthesis mechanisms
- Microbial Metabolic Engineering and Bioproduction
- Animal Virus Infections Studies
- Immunotherapy and Immune Responses
- Viral gastroenteritis research and epidemiology
- Enzyme Structure and Function
- Glycosylation and Glycoproteins Research
- Bioinformatics and Genomic Networks
- COVID-19 Clinical Research Studies
- vaccines and immunoinformatics approaches
- CAR-T cell therapy research
- Virus-based gene therapy research
- Computational Drug Discovery Methods
- Malaria Research and Control
- interferon and immune responses
- T-cell and B-cell Immunology
- Medication Adherence and Compliance
- Parasites and Host Interactions
- Chemical Synthesis and Analysis
- Immune Cell Function and Interaction
- Pharmacology and Obesity Treatment
- Biomedical Text Mining and Ontologies
Barcelona Supercomputing Center
2019-2024
University of Basel
2018-2024
Universitat Politècnica de Catalunya
2019-2024
University Hospital of Basel
2021-2024
Med Discovery (Switzerland)
2023
PIQUR Therapeutics (Switzerland)
2022-2023
SIB Swiss Institute of Bioinformatics
2018
Istituto Pasteur
2011-2018
Sapienza University of Rome
2011-2018
Technical University of Denmark
2014
Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated workflows servers simplify streamline homology process, also allowing users without a specific computational expertise generate reliable models have easy access results, their visualization interpretation. Here, we present update SWISS-MODEL server, which pioneered field of...
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 Motivation Understanding the molecular mechanisms of thermal stability is a challenge in protein biology. Indeed, knowing temperature at which proteins are stable has important theoretical implications, intimately linked with properties native fold, and wide range potential applications from drug design to optimization enzyme activity. Results Here, we present novel graph-theoretical framework assess based on structure without any priori information. In this approach describe as...
The emerging SARS-CoV-2 variants of concern (VOCs) may display enhanced transmissibility, more severity and/or immune evasion; however, the pathogenesis these new VOCs in experimental models or potential infection other animal species is not completely understood. Here we infected K18-hACE2 transgenic mice with B.1, B.1.351/Beta, B.1.617.2/Delta and BA.1.1/Omicron isolates demonstrated heterogeneous infectivity pathogenesis. B.1.351/Beta variant was most pathogenic, while led to lower viral...
Abstract Haematopoietic stem cell (HSC) transplantation (HSCT) is the only curative treatment for a broad range of haematological malignancies, but standard care relies on untargeted chemotherapies and limited possibilities to treat malignant cells after HSCT without affecting transplanted healthy 1 . Antigen-specific cell-depleting therapies hold promise much more targeted elimination diseased cells, as witnessed in past decade by revolution clinical practice B malignancies 2 However,...
There is a wide interest in designing peptides able to bind specific region of protein with the aim interfering known interaction or as starting point for design inhibitors. Here we describe PepComposer, new pipeline computational binding given surface. PepComposer only requires target structure and an approximate definition site input. We first retrieve set peptide backbone scaffolds from monomeric proteins that harbor same arrangement interest. Next, optimal sequences identified scaffolds....
Targeted eradication of transformed or otherwise dysregulated cells using monoclonal antibodies (mAb), antibody–drug conjugates (ADC), T cell engagers (TCE), chimeric antigen receptor (CAR) is very effective for hematologic diseases. Unlike the breakthrough progress achieved B malignancies, there a pressing need to find suitable antigens myeloid malignancies. CD123, interleukin-3 (IL-3) alpha-chain, highly expressed in various hematological including acute leukemia (AML). However, shared...
Abstract Background The co-administration of drugs known to interact greatly impacts morbidity, mortality, and health economics. This study aims examine the drug–drug interaction (DDI) phenomenon with a large-scale longitudinal analysis age gender differences found in drug administration data from three distinct healthcare systems. Methods analyzes administrations population-wide electronic records Blumenau (Brazil; 133 K individuals), Catalonia (Spain; 5.5 M Indianapolis (USA; 264...
PIGSpro is a significant upgrade of the popular PIGS server for prediction structure immunoglobulins. The software has been completely rewritten in python following similar pipeline as original method, but including, at various steps, relevant modifications found to improve its accuracy, demonstrated here. steps include selection appropriate framework predicting conserved regions molecule by homology; target template alignment this portion molecule; main chain conformation hypervariable...
Background. Chronic Obstructive Pulmonary Disease (COPD) is a heterogeneous condition. We hypothesized that the unbiased integration of different COPD lung omics using novel multi-layer approach may unravel mechanisms associated with clinical characteristics. Methods. profiled mRNA, miRNA and methylome in tissue samples from 135 former smokers COPD. For each omic (layer) we built patient network based on molecular similarity. The three networks were used to build network, optimization...
The biological and functional significance of selected Critical Assessment Techniques for Protein Structure Prediction 14 (CASP14) targets are described by the authors structures. highlight most relevant features target proteins discuss how well these were reproduced in respective submitted predictions. overall ability to predict three-dimensional structures has improved remarkably CASP14, many difficult modeled with impressive accuracy. For first time history CASP, experimentalists not only...
Abstract Background Neoantigens are patient- and tumor-specific peptides that arise from somatic mutations. They stand as promising targets for personalized therapeutic cancer vaccines. The identification process neoantigens has evolved with the use of next-generation sequencing technologies bioinformatic tools in tumor genomics. However, in-silico strategies selecting immunogenic still have very low accuracy rates, since they mainly focus on predicting peptide binding to Major...
Monitoring resistance phenotypes for Plasmodium falciparum, using in vitro growth assays, and relating findings to parasite genotype has proved particularly challenging the study of artemisinins.Plasmodium falciparum isolates cultured from 28 returning travellers diagnosed with malaria were assessed sensitivity artemisinin, artemether, dihydroartemisinin artesunate related mutations pfatp6 pfmdr1.Resistance artemether was significantly associated a haplotype encoding two amino acid...
In nanopore sensing experiments, the properties of molecules are probed by variation ionic currents flowing through nanopore. this context, electronic and single-layer thickness graphene constitute a major advantage for molecule characterization. Here we analyze translocation pathway thioredoxin protein across nanopore, related currents, integrating two nonequilibrium molecular dynamics methods with bioinformatic structural analysis. To obtain qualitative picture process to identify salient...
Abstract As a result of the advent high-throughput technologies, there has been rapid progress in our understanding genetics underlying biological processes. However, despite such advances, genetic landscape human diseases only marginally disclosed. Exploiting present availability large amounts and phenotypic data, we can use current disease to train machine learning models predict novel factors associated with disease. To this end, developed DGLinker, webserver for prediction candidate...
Abstract Motivation: Predicting the structure of protein loops is very challenging, mainly because they are not necessarily subject to strong evolutionary pressure. This implies that, unlike rest protein, standard homology modeling techniques effective in their structure. However, often involved function, hence inferring important for predicting as well function. Results: We describe a method, LoopIng, based on Random Forest automated learning technique, which, given target loop, selects...
Abstract Hypocotyl elongation is influenced by light and hormones, but the molecular mechanisms underlying this process are not yet fully elucidated. We had previously suggested that Arabidopsis DOF transcription factor DAG1 may be a negative component of mechanism light-mediated inhibition hypocotyl elongation, as light-grown dag1 knock-out mutant seedlings show significant shorter hypocotyls than wild type. By using high-throughput RNA-seq, we compared transcriptome profile type seedlings....
Abstract Motivation: Antibodies are able to recognize a wide range of antigens through their complementary determining regions formed by six hypervariable loops. Predicting the 3D structure these loops is essential for analysis and reengineering novel antibodies with enhanced affinity specificity. The canonical model allows high accuracy prediction five third loop heavy chain, H3, hardest predict because its diversity in structure, length sequence composition. Results: We describe method,...
Abstract We describe here a superposition free method for comparing the surfaces of antibody binding sites based on Zernike moments and show that they can be used to quickly compare cluster sets antibodies. The clusters provide information about nature bound antigen that, when combined with predicting number direct contacts, allows discrimination between protein non-protein antibodies an accuracy 76%. This is relevance in several aspects science, example select framework combinatorial library.
With the spread of new variants severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is a need to assess protection conferred by both previous infections and current vaccination. Here we tested neutralizing activity infected and/or vaccinated individuals against pseudoviruses expressing spike original SARS-CoV-2 isolate Wuhan-Hu-1 (WH1), D614G mutant B.1.1.7 variant. Our data show that parameters natural infection (time from nature infecting variant) determined...
We present the results of assessment intramolecular residue-residue contact and distance predictions from groups participating in 14th round CASP experiment. The performance prediction methods was evaluated with measures used previous CASPs, while were assessed based on a new protocol, which considers individual pairs as well whole predicted matrix, using graph-based framework. evaluation indicate that by tFold framework, TripletRes DeepPotential most accurate both categories. With regards...