• Publications
  • Influence
CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
TLDR
A new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations is presented, and analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. Expand
CAVER: a new tool to explore routes from protein clefts, pockets and cavities
TLDR
An algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent is developed and implemented for the CAVER program. Expand
PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations
TLDR
This study constructed three independent datasets by removing all duplicities, inconsistencies and mutations previously used in the training of evaluated prediction tools, and returned results for all mutations, confirming that consensus prediction represents an accurate and robust alternative to the predictions delivered by individual tools. Expand
HotSpot Wizard: a web server for identification of hot spots in protein engineering
TLDR
The HotSpot Wizard server should be useful for protein engineers interested in exploring the structure of their favourite protein and for the design of mutations in site-directed mutagenesis and focused directed evolution experiments. Expand
CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures
TLDR
CAVER Analyst is a software tool for calculation, analysis and real-time visualization of access tunnels and channels in static and dynamic protein structures that provides an intuitive graphic user interface for setting up the calculation and interactive exploration of identified tunnels/channels and their characteristics. Expand
High occurrence of BRCA1 intragenic rearrangements in hereditary breast and ovarian cancer syndrome in the Czech Republic
TLDR
Using MLPA, mutations were detected in 6% of high-risk patients previously designated as BRCA1/2 mutation-negative and the breakpoints of five out of six large deletions detected in Czech patients are novel. Expand
Phylogenetic analysis of haloalkane dehalogenases
TLDR
Light is shed on the evolutionary history of HLDs and a structural framework for designing enzymes with new specificities is provided, including a common conserved core as well as a set of residues that characterizes each HLD subfamily. Expand
CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules
TLDR
The principles of the CAVER 3.0 algorithms for the identification and analysis of properties of transport pathways both in static and dynamic structures are described and the improved clustering solution for finding tunnels in macromolecules is introduced. Expand
PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions
TLDR
A user-friendly web interface was developed that provides easy access to the five tools’ predictions, and their consensus scores, in a user-understandable format tailored to the specific features of different categories of variations. Expand
Molecular Dissection of Interactions between Rad51 and Members of the Recombination-Repair Group
TLDR
A new strategy to screen for mutations which cause specific disruption of the interaction between certain proteins in the complex, leaving other interactions intact is described, suggesting that dynamic changes within the Rad51 protein may contribute to an ordered reaction process. Expand
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