A5055976242- Enzyme Structure and Function
- Protein Structure and Dynamics
- Advanced Proteomics Techniques and Applications
- Genomics and Rare Diseases
- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Receptor Mechanisms and Signaling
- vaccines and immunoinformatics approaches
- Machine Learning in Bioinformatics
- Genomics and Chromatin Dynamics
- Biological Research and Disease Studies
- Genetics, Bioinformatics, and Biomedical Research
- Data Visualization and Analytics
- Health, Environment, Cognitive Aging
- Neuropeptides and Animal Physiology
- Pancreatic function and diabetes
- Molecular Biology Techniques and Applications
- Biochemical and Molecular Research
- Glycosylation and Glycoproteins Research
- Gene expression and cancer classification
- Computational Drug Discovery Methods
- Bioinformatics and Genomic Networks
- Mass Spectrometry Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Microbial Natural Products and Biosynthesis
Radboud University Medical Center
2009-2023
Radboud University Nijmegen
2009-2023
Radboud Institute for Molecular Life Sciences
2010-2019
University Medical Center
2019
Universidade Federal de São Paulo
2010
We present a series of databanks (http://swift.cmbi.ru.nl/gv/facilities/) that hold information is computationally derived from Protein Data Bank (PDB) entries and might augment macromolecular structure studies. These run parallel to the PDB, i.e. they have one entry per PDB entry. Several well-established such as HSSP, PDBREPORT PDB_REDO been updated and/or improved. The software creates DSSP databank, for example, has rewritten better cope with π-helices. A large number added aid...
The growing availability of human genetic variation has given rise to novel methods measuring tolerance that better interpret variants unknown significance. We recently developed a concept based on protein domain homology in the genome improve variant interpretation. For this purpose, we mapped population from Exome Aggregation Consortium (ExAC) and pathogenic mutations Human Gene Mutation Database (HGMD) onto Pfam domains. aggregation these data across homologous domains into meta-domains...
The GPCRDB is a Molecular Class-Specific Information System (MCSIS) that collects, combines, validates and disseminates large amounts of heterogeneous data on G protein-coupled receptors (GPCRs). contains experimental sequences, ligand-binding constants, mutations oligomers, as well many different types computationally derived such multiple sequence alignments homology models. provides access to the via number methods. It offers visualization analysis tools, query systems. updated...
Abstract The growing availability of human genetic variation has given rise to novel methods measuring tolerance that better interpret variants unknown significance. We recently developed a concept based on protein domain homology in the genome improve variant interpretation. For this purpose we mapped population from Exome Aggregation Consortium (ExAC) and pathogenic mutations Human Gene Mutation Database (HGMD) onto Pfam domains. aggregation these data across homologous domains into...
Cancer immunotherapies show promise in eliminating tumors, but identifying tumor peptides that bind patient MHC proteins to trigger immune responses remains challenging. The vast peptide-MHC diversity makes experimental identification costly, emphasizing the need for computational predictions. To address scalability, we introduce SwiftMHC, an attention network MHC-bound and generating all-atom 3D structures simultaneously. SwiftMHC processes cases 0.01 2.2 seconds on a single A100 GPU,...
We present DeepRank2, a deep learning (DL) framework geared towards making predictions on 3D protein structures for variety of biologically relevant applications.Our software can be used predicting structural properties in drug design, immunotherapy, or designing novel proteins, among other fields.DeepRank2 allows transformation and storage representations both protein-protein interfaces (PPIs) single-residue variants (SRVs) into either graphs volumetric grids containing physico-chemical...
Predicting pathogenicity of missense variants in molecular diagnostics remains a challenge despite the available wealth data, such as evolutionary information, and tools to integrate that data. We describe DeepRank-Mut, configurable framework designed extract learn from physicochemically relevant features amino acids surrounding 3D space. For each variant, various atomic residue-level are extracted its structural environment, including sequence conservation scores acids, stored multi-channel...
G-protein-coupled receptors (GPCRs) constitute a large family of cell surface that are involved in wide range physiological and pathological processes, targets for many therapeutic interventions. However, genetic models the rat, one most widely used model organisms pharmacological research, largely lacking. Here, we applied N-ethyl-N-nitrosourea (ENU)-driven target-selected mutagenesis to generate an vivo GPCR mutant collection rat. A pre-selected panel 250 human homologs was screened...
The NewProt protein engineering portal is a one-stop-shop for in silico engineering. It gives access to large number of servers that compute wide variety structure characteristics supporting work on the modification proteins through introduction (multiple) point mutations. results can be inspected multiple visualizers. HOPE software included indicate mutations with possible undesired side effects. Hotspot Wizard embedded design modify proteins' activity, specificity, or stability. freely...
Abstract We describe a series of databases and tools that directly or indirectly support biomedical research on macromolecules, with focus their applicability in protein structure bioinformatics research. DSSP, determines secondary structures proteins, has been updated to work well extremely large multiple formats. The PDBREPORT database lists anomalies remade remove many small problems. These reports are now available as PDF‐formatted files computer‐readable summary. VASE software added...
It is much easier to determine a protein’s sequence than its three dimensional structure and consequently homology modeling will be an essential aspect of most studies that require 3D protein data. Homology templates tend PDB files. About 88% all structures in the have been determined with X-ray crystallography, thus are based on crystals by necessity hold non-natural packing contacts accordance crystal symmetry. Active site residues, residues involved intermolecular interactions, get...