A5037343661- Protein Structure and Dynamics
- Microbial Metabolic Engineering and Bioproduction
- Enzyme Structure and Function
- Pharmacogenetics and Drug Metabolism
- Genetics, Bioinformatics, and Biomedical Research
- Enzyme Catalysis and Immobilization
- Microbial Metabolites in Food Biotechnology
- Photosynthetic Processes and Mechanisms
- Antimicrobial Peptides and Activities
- Eicosanoids and Hypertension Pharmacology
- Education, Psychology, and Social Research
- Biochemical and Structural Characterization
- Advanced Proteomics Techniques and Applications
- Bioinformatics and Genomic Networks
- Cancer Treatment and Pharmacology
- Hormonal Regulation and Hypertension
- Nutrition, Genetics, and Disease
- Mass Spectrometry Techniques and Applications
- Algorithms and Data Compression
- Machine Learning in Bioinformatics
- Antimicrobial agents and applications
- Protein Interaction Studies and Fluorescence Analysis
- vaccines and immunoinformatics approaches
- Cell Image Analysis Techniques
- Genomics and Rare Diseases
Veterinary Research Institute
2023-2024
Masaryk University
2009-2023
RECETOX
2012-2018
San Diego Supercomputer Center
2017
University of California, San Diego
2017
University of West Bohemia
2014
University Hospital Brno
2012
St. Anne's University Hospital Brno
2012
Tunnels and channels facilitate the transport of small molecules, ions water solvent in a large variety proteins. Characteristics individual pathways, including their geometry, physico-chemical properties dynamics are instrumental for understanding structure-function relationships these proteins, design new inhibitors construction improved biocatalysts. CAVER is software tool widely used identification characterization pathways static macromolecular structures. Herein we present version...
Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the coding regions are frequently associated with development various diseases. Computational tools for prediction effects mutations on protein function very important analysis single and their prioritization experimental characterization. Many computational already widely employed this purpose. Unfortunately, comparison further improvement is hindered by large overlaps between training datasets...
Abstract Motivation Studying the transport paths of ligands, solvents, or ions in transmembrane proteins and with buried binding sites is fundamental to understanding their biological function. A detailed analysis structural features influencing also important for engineering biomedical biotechnological applications. Results CAVER Analyst 2.0 a software tool quantitative real-time visualization tunnels channels static dynamic structures. This version provides users many new functions,...
HotSpot Wizard is a web server for automatic identification of ‘hot spots’ engineering substrate specificity, activity or enantioselectivity enzymes and annotation protein structures. The implements the protocol, which targets evolutionarily variable amino acid positions located in active site lining access tunnels. mutagenesis are selected through integration structural, functional evolutionary information obtained from: (i) databases RCSB PDB, UniProt, PDBSWS, Catalytic Site Atlas nr NCBI...
The biological function of a macromolecule often requires that small molecule or ion is transported through its structure. transport pathway leads void spaces in the properties pathways change significantly time; therefore, analysis trajectory from molecular dynamics rather than single static structure needed for understanding pathways. identification and are challenging because high complexity diversity macromolecular shapes, thermal motion their atoms, large amount conformations to...
Abstract Summary: The transport of ligands, ions or solvent molecules into proteins with buried binding sites through the membrane is enabled by protein tunnels and channels. CAVER Analyst a software tool for calculation, analysis real-time visualization access channels in static dynamic structures. It provides an intuitive graphic user interface setting up calculation interactive exploration identified tunnels/channels their characteristics. Availability Implementation: multi-platform...
Recent advances in experimental techniques have led to a rapid growth complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates challenge for visualization analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow transfer, parse, hard incorporate into third-party software tools. Here, we present new binary compressed data representation, MacroMolecular Transmission Format, MMTF, well...
Abstract The use of enzymes for biocatalysis can be significantly enhanced by using organic cosolvents in the reaction mixtures. Selection cosolvent type and concentration range an enzymatic is challenging requires extensive empirical testing. An understanding protein–solvent interaction could provide a theoretical framework rationalising selection process. Here, behaviour three model (haloalkane dehalogenases) was investigated presence representative (acetone, formamide, isopropanol)....
Abstract Antimicrobial peptides, including the human cathelicidin LL-37, offer a possible solution to global problem of bacterial resistance antibiotics. LL-37 peptide has potent antimicrobial effects against current multi-drug resistant strains. The itself is also characterized by very diverse range immunomodulatory effects. aim this study was produce antimicrobially active in E. coli high yields using an own expression system pUbEx100 with fusion protein ubiquitin. results showed that...
Abstract Recent advances in experimental techniques have led to a rapid growth complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates challenge for visualization analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow transfer, parse, hard incorporate into third-party software tools. Here, we present new binary compressed data representation, MacroMolecular Transmission Format, MMTF, well...