A5060799515- Protein Structure and Dynamics
- Enzyme Structure and Function
- Microbial Metabolic Engineering and Bioproduction
- Pharmacogenetics and Drug Metabolism
- Berberine and alkaloids research
- Bioinformatics and Genomic Networks
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Phylogenetic Studies
- Plant-based Medicinal Research
- Advanced Proteomics Techniques and Applications
- Chemical synthesis and alkaloids
- Scientific Computing and Data Management
- Chemical Reactions and Isotopes
- Cell Image Analysis Techniques
- Machine Learning in Bioinformatics
- Microbial Natural Products and Biosynthesis
- Advanced Synthetic Organic Chemistry
- Chromatography in Natural Products
- Plant tissue culture and regeneration
- RNA and protein synthesis mechanisms
- Synthesis and bioactivity of alkaloids
- bioluminescence and chemiluminescence research
- Advanced Electron Microscopy Techniques and Applications
- Enzyme Catalysis and Immobilization
European Bioinformatics Institute
2023-2025
Masaryk University
2016-2023
Central European Institute of Technology
2017-2023
Central European Institute of Technology – Masaryk University
2017-2023
Abstract With the ever‐expanding toolkit of molecular viewers, ability to visualize macromolecular structures has never been more accessible. Yet, idiosyncratic technical intricacies across tools and integration complexities associated with handling structure annotation data present significant barriers seamless interoperability steep learning curves for many users. The necessity reproducible visualizations is at forefront current challenges. Recently, we introduced MolViewSpec (homepage:...
Abstract Data visualization is a pivotal component of structural biologist’s arsenal. The Mol* Viewer makes molecular visualizations available to broader audiences via most web browsers. While provides wide range functionality, it has steep learning curve and only JavaScript interface. To enhance the accessibility usability web-based visualization, we introduce MolViewSpec (molstar.org/mol-view-spec), standardized approach for defining that decouples definition complex scenes from their...
Abstract Protein structural families are groups of homologous proteins defined by the organization secondary structure elements (SSEs). Nowadays, many contain vast numbers structures, and SSEs can help to orient within them. Communities around specific protein have even developed specialized SSE annotations, always assigning same name equivalent in proteins. A detailed analysis provides an overview studied family enriches any particular at hand. We a workflow for anatomy family. applied this...
Secondary structures provide a deep insight into the protein architecture. They can serve for comparison between individual family members. The most straightforward way how to deal with secondary structure is its visualization using 2D diagrams. Several software tools generation of diagrams were developed. Unfortunately, they create based on only single protein. Therefore, two proteins from one markedly differ. For this reason, we developed 2DProts database, which contains all domains CATH...
Abstract Segmentation helps interpret imaging data in a biological context. With the development of powerful tools for automated segmentation, public repositories have added support sharing and visualizing segmentations, creating need interactive web-based visualization 3D volume segmentations. To address ongoing challenge integrating multimodal data, we developed Mol* Volumes Segmentations (Mol*VS), which enables interactive, cellular supported by macromolecular annotations. Mol*VS is fully...
Abstract Summary Every protein family has a set of characteristic secondary structures. However, due to individual variations, single structure is not enough represent the whole family. OverProt can create consensus, showing general fold as well its variation. Our server provides precomputed results for all CATH superfamilies and user-defined computations, visualized by an interactive viewer, which shows element type, length, frequency occurrence, spatial variability β-connectivity....
LiteMol is a unique and comprehensive macromolecular structure viewer which through real-time data delivery enables even large structures to be visualised in the browser platform independent manner.LiteMol fully integrated into webpages at Protein Data Bank Europe (PDBe.org),a founder member of wwPDB.LiteMol composed 3D molecular Viewer, services CoordinateServer DensityServer, format called BinaryCIF.LiteMol Viewer provides interactive web-browser based visualisation together with maps...
Abstract Protein structural families are groups of homologous proteins defined by the organization secondary structure elements (SSEs). Nowadays, many contain vast numbers structures, and SSEs can help to orient within them. Communities around specific protein have even developed specialized SSE annotations, always assigning same name equivalent in proteins. A detailed analysis provides an overview studied family enriches any particular at hand. We a workflow for anatomy family. applied this...
Summary: PDBImages is an innovative, open-source Node.js package that harnesses the power of popular macromolecule structure visualization software Mol*. Designed for use by scientific community, provides a means to generate high-quality images PDB and AlphaFold DB models. Its unique ability render save directly files in browserless mode sets it apart, offering users streamlined, automated process macromolecular visualization. Here, we detail implementation PDBImages, enumerating its diverse...
PDBImages is an innovative, open-source Node.js package that harnesses the power of popular macromolecule structure visualization software Mol*. Designed for use by scientific community, provides a means to generate high-quality images PDB and AlphaFold DB models. Its unique ability render save directly files in browserless mode sets it apart, offering users streamlined, automated process macromolecular visualization. Here, we detail implementation PDBImages, enumerating its diverse image...