Welcome & What can we offer
Loschmidt Laboratories (LL), affiliated to the Masaryk University, provides an expertise in the field of protein engineering and metabolic engineering. The laboratories were founded in 2004 and provide unique software solutions for analysis of protein structures, prediction of the effect of mutations of human health and design of robust protein catalysts. The group wish to understand the structure-function relationships of proteins and improve their functionalities for biotechnologies. The group also studies molecular mechanisms of neurodegenerative diseases, including Alzheimer’s and Parkinson’s disease.
How can you access
Head: Jiří Damborský (firstname.lastname@example.org)
Staff: Lenka Sumbalová, Adam Jurčík, Lukáš Chrást, Gabriela Daňková
Please, fill in the short registration form
The information will be used (i) for your identification as a customer of our infrastructure (ii) for contacting you in case we will need more information about your samples.
FAST KINETICS: Stopped-flow and rapid quench flow analysis
Fast kinetic methods allow to study mechanisms of enzymatic reactions and biomolecular interactions. This analysis for example provides information on the slowest rate-limiting steps, which needs to be modified in order to improve effectivity of biological systems. The data must be collected with a very high precision and mathematically analysed to obtain a biologically meaningful information.
THERMODYNAMICS: Circular dichroism spectrometry analysis
This analysis provides information about structure and conformation of proteins in a solution. Analysis carried out with a temperature ramp allows study of thermodynamic properties of proteins and determination of their melting temperatures (Tm). Method is sufficiently rapid for analysis of the effect of mutations on composition of secondary elements in protein structure and thermodynamic stability.
THERMODYNAMICS: Microcalorimetric analysis
This method allows for real-time monitoring of thermodynamic and kinetic properties of biomolecules. The method is suitable for example for study of protein-ligand interactions, protein unfolding and thermodynamic stability of protein and DNA samples. Both isothermal microcalorimetry (IMC) and differential scanning calorimetry (DSC) are available for analysis of protein and DNA samples.
SOFTWARE: Rational design of mutations and smart libraries in protein engineering
This is a web server for automated identification of hot spots and design of smart libraries for engineering proteins’ stability, catalytic activity, substrate specificity and enantioselectivity. The server implements four different established protein engineering strategies, enabling the user to selectively target sites affecting the protein’s stability and catalytic properties. A graphical interface provides an intuitive and comprehensive overview of the results of the analysis. The resulting pipeline of twenty integrated tools and three databases represents a unique one-stop solution that makes library design accessible even to users with no prior knowledge of bioinformatics.
SOFTWARE: Analysis of tunnels and channels in biomolecules
This software tool is widely used for the identification and characterization of transport pathways in macromolecular structures. A new version enables automatic analysis of tunnels and channels in large ensembles of protein conformations since the analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. The program paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform JAVA command-line application or PyMol plug-in.
SOFTWARE: Rational design of tunnels and channels in biomolecules
This new software tool provides an interface between CAVER software, suitable for analysis of protein tunnels & channels, and the program ROSETTA, suitable for computational design of protein molecules, optimization of their structures and evaluation of their stabilities. The users can use this software for structure-based design of opening or closing of protein tunnels, which is a novel concept for engineering of proteins with modified activity, stability or substrate specificity. Stand-alone version is available as PyMol plug-in upon request from developers.
SOFTWARE: Analysis of the effect of mutations on human health
This suite of programs provides users with the prediction of the effect of mutations on human health at protein and DNA level. The benchmark dataset containing over 43,000 mutations was employed for the unbiased evaluation of eight established prediction tools: MAPP, nsSNPAnalyzer, PANTHER, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT and SNAP. The six best performing tools were combined into a consensus classifier PredictSNP, resulting into significantly improved prediction performance and robustness. PredictSNP2 provides easy access to binary predictions and uniform confidence values for the five best-performing prediction tools and their consensus. These predictions are supplemented with information gathered from eight publicly available databases. PredictSNP2 extends the scope of genome analysis to the level of nucleotide substitutions that enables to identify disease-related variants within the whole genome.