Vyhledávání publikací

Vybrané publikace/výsledky

In vitro protein and metabolic engineering of a biodegradation pathway (2011)
CAVER Analyst 1.0: Graphic tool for interactive visualization and analysis of tunnels and channels in protein structures (2014)
Caver Analyst 1.0 (2014)
Site-specific Analysis of Protein Hydration Based on Unnatural Amino Acid Fluorescence. (2015)
Balancing the Stability-Activity Trade-off by Fine-Tuning Dehalogenase Access Tunnels. (2015)
FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants (2015)
Thermostable FGF2 Polypeptide, Use Thereof (2020)
Accelerated Visualization of Transparent Molecular Surfaces in Molecular Dynamics (2016)
Interactive Exploration of Ligand Transportation through Protein Tunnels (2017)
Individuální rozdíly v učení se cizím jazykům: specifická situace neslyšících (2017)
Watergate: Visual Exploration of Water Trajectories in Protein Dynamics (2017)
CaverDock 1.0 (2017)
Recombinant enzyme gamma-hexachlorocyclohexane dehydrochlorinase LinA01 carrying thermostabilizing mutations by energy-based approach (2017)
Recombinant enzyme haloalkane dehalogenase DhaA101 carrying thermostabilizing mutations by evolution-based approach (2017)
Recombinant enzyme haloalkane dehalogenase DhaA112 carrying thermostabilizing mutations by energy-based approach (2017)
Recombinant enzyme haloalkane dehalogenase DhaA115 carrying thermostabilizing mutations by combine approach (2017)
Recombinant enzyme halohydrin dehalogenase HheC-LT02 carrying thermostabilizing mutations. (2017)
HTS 1.0 (2017)
Recombinant enzyme halohydrin dehalogenase HheC-DJ carrying thermostabilizing mutations. (2017)
NewProt – a Protein Engineering Portal (2017)
Different Structural Origins of the Enantioselectivity of Haloalkane Dehalogenases toward Linear beta-Haloalkanes: Open–Solvated versus Occluded–Desolvated Active Sites (2017)
FireProt: Web Server for Automated Design of Thermostable Proteins (2017)
Structure-function Relationships and Engineering of Haloalkane Dehalogenases. (2017)
FireProt 1.0 (2017)
NewProt 1.0 (2017)
Computational Enzyme Design of Haloalkane Dehalogenases for Yperite Degradation (2018)
Computer-assisted engineering of hyperstable fibroblast growth factor 2 (2018)
Sampling-based Motion Planning for Tracking Evolution of Dynamic Tunnels in Molecular Dynamics Simulations (2019)
CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories (2018)
Academic mobilities of students with hearing impairment: Welcoming the challenges with specialized online course of written English (2018)
Visual Analysis of Ligand Trajectories in Molecular Dynamics (2019)
14th ESSE Conference (2018)
Molecular Gating of an Engineered Enzyme Captured in Real Time (2018)
Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization (2018)
Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site (2018)
CalFitter: a web server for analysis of protein thermal denaturation data (2018)
HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information (2018)
CaverDock: A Novel Method for the Fast Analysis of Ligand Transport (2020)
Bilaminární kožní dermální náhrada: Vliv stabilního FGF2 na kapilární denzitu sledovanou pomocí modelů ex-ovo a in vivo (2019)
Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization (2019)
Development of an innovative nanostructured dermal matrix in combination with a hyperstable form of growth factor for fibroblasts (FGF2): Ex ovo and in vivo study (2019)
CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels (2019)
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport (2019)
Structural Biology and Protein Engineering of Thrombolytics (2019)
Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts (2019)
Fluorescent pH Indicators for Neutral to Near-Alkaline Conditions Based on 9-Iminopyronin Derivatives (2019)
Collagen-based dermal substitute with stable fibroblast growth factor 2 (FGF2): ex ovo and in vivo impact on neovascularization (2019)
Controlled Oil/Water Partitioning of Hydrophobic Substrates Extending the Bioanalytical Applications of Droplet-Based Microfluidics (2019)
New collagen foam with nanotechnological modification as bi-layer dermal substitute: Influence of stable FGF2 on capillary density in different animal models (2019)
Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway (2019)
Testování bilaminární kožní náhrady obohacené stabilním FGF2 na ex ovo a in vivo modelech (2019)
Fast Screening of Inhibitor Binding/Unbinding using Novel Software Tool CaverDock (2019)
Nanopatterning Glass Surface For Localization Of Embryonic Stem Cells (2019)
Deaf learners' processing of English textbook material : An eye-tracking study (2020)
Fibroblast Growth Factor 2 Protein Stability Provides Decreased Dependence on Heparin for Induction of FGFR Signaling and Alters ERK Signaling Dynamics (2019)
A benchmark set of highly-efficient CUDA and OpenCL kernels and its dynamic autotuning with Kernel Tuning Toolkit (2020)
Computational Study of Protein-Ligand Unbinding for Enzyme Engineering (2019)
Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase (2019)
Development of Fluorescent Assay for Monitoring of Dehalogenase Activity (2019)
Computational Design of Stable and Soluble Biocatalysts (2019)
Crystal structure of the cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5 (2019)
Transhalogenation Catalysed by Haloalkane Dehalogenases Engineered to Stop Natural Pathway at Intermediate (2019)
Engineering enzyme access tunnels (2019)
Crystallization and Crystallographic Analysis of a Bradyrhizobium Elkanii USDA94 Haloalkane Dehalogenase Variant with an Eliminated Halide-Binding Site (2019)
Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic Bacterium Marinobacter sp. ELB17 (2019)
An Ultrasensitive Fluorescence Assay for the Detection of Halides and Enzymatic Dehalogenation (2020)
Machine Learning in Enzyme Engineering (2020)
ACCELERATION AND GLOBAL CONVERGENCE OF A FIRST-ORDER PRIMAL-DUAL METHOD FOR NONCONVEX PROBLEMS (2019)
Foreign Language Learning Experiences of Deaf and Severely Hard-of-Hearing Czech University Students (2019)
Functional switching based on altered enzyme flexibility via InDel mutagenesis of a reconstructed ancestor (2019)
Caver web: identification of tunnels and channels in proteins and analysis of ligand transport (2019)
DockVis: Visual Analysis of Molecular Docking Trajectories (2020)
Engineering of enzyme gating driven by molecular dynamics, transient kinetics, and single molecule spectroscopy (2018)
Transcription and Translation Inhibitors in Cancer Treatment (2020)
Exploiting historical data: Pruning autotuning spaces and estimating the number of tuning steps (2020)
ChemVA: Interactive Visual Analysis of Chemical Compound Similarity in Virtual Screening (2021)
Exploring Protein Folding Space with Neural Network Guided Simulations (2020)
Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst (2020)
EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities (2020)
A Haloalkane Dehalogenase from Saccharomonospora viridis Strain DSM 43017, a Compost Bacterium with Unusual Catalytic Residues, Unique (S)-Enantiopreference, and High Thermostability (2020)
Exploration of enzyme diversity: High-throughput techniques for protein production and microscale biochemical characterization (2020)
Online English for International Mobilities: A course for students (2020)
Fostering autonomy in learners with special needs: a specialized e-learning course (2020)
Seminář pro učitele angličtiny pracující s neslyšícími a nedoslýchavými studenty (2020)
Surface-enhanced Raman Spectroscopy in Microfluidic Chips for Directed Evolution of Enzymes and Environmental Monitoring (2019)
The impact of tunnel mutations on enzymatic catalysis depends on the tunnel-substrate complementarity and the rate-limiting step (2020)
Fluorescent substrates for haloalkane dehalogenases: Novel probes for mechanistic studies and protein labeling (2020)
Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics (2020)
Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family (2020)
4D-GRAPHS (2021)
Simulation of Ligand Transport in Receptors Using CaverDock (2021)
Screening of Natural Compounds as P-Glycoprotein Inhibitors against Multidrug Resistance (2021)
Thermostable FGF2 Polypeptide, Use Thereof (2021)
Development and Testing of Thrombolytics in Stroke (2021)
Promiscuous Dehalogenase Activity of the Epoxide Hydrolase CorEH from Corynebacterium sp. C12 (2021)
Structure-Function Relationships and Engineering of Haloalkane Dehalogenases (2019)
FireProt(DB): database of manually curated protein stability data (2021)
Substrate inhibition by the blockage of product release and its control by tunnel engineering (2021)
Computational design of enzymes for biotechnological applications (2021)
SoluProt: prediction of soluble protein expression in Escherichia coli (2021)
Kernel Tuning Toolkit 2.0 (2021)
Exploring mechanism of enzyme catalysis by on-chip transient kinetics coupled with global data analysis and molecular modeling (2021)
VRdeo: Creating engaging educational material for asynchronous student-teacher exchange using virtual reality (2021)
Screening of world approved drugs against highly dynamical spike glycoprotein of SARS-CoV-2 using CaverDock and machine learning (2021)
Using hardware performance counters to speed up autotuning convergence on GPUs (2022)
Engineering the protein dynamics of an ancestral luciferase (2021)
Searching CUDA code autotuning spaces with hardware performance counters: data from benchmarks running on various GPU architectures (2021)
Úskalí laboratorních metod v ovariálním skríninku - doba "-omická"? (2020)
Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers (2021)
FireProt(ASR): A Web Server for Fully Automated Ancestral Sequence Reconstruction (2021)
Complex simulation workflows in containerized high-performance environment (2021)
Property Map Collective Variable as a Useful Tool for a Force Field Correction (2022)
Designované a syntetizované geny kódující nově zkonstruované proteinové katalyzátory (luciferázy) s ověřenými vlastnostmi (2021)
Thermostable FGF2 polypeptide, use thereof (2021)
Improving ligand transport trajectory within flexible receptor in CaverDock (2022)
PDBe-KB: collaboratively defining the biological context of structural data (2022)
Computer-aided engineering of staphylokinase toward enhanced affinity and selectivity for plasmin (2022)
Deep Insights into the Specific Evolution of Fungal Hybrid B Heme Peroxidases (2022)
Tools for computational design and high-throughput screening of therapeutic enzymes (2022)
Mechanism-Based Design of Efficient PET Hydrolases (2022)
Engineering protein dynamics for the understanding of divergent evolution of the Renilla luciferase (2021)
Computational enzyme design for metabolic engineering (2021)
Fast approximative methods for study of ligand transport and rational design of improved enzymes for biotechnologies (2022)
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering (2022)
A Nonconventional Archaeal Fluorinase Identified by In SilicoMining for Enhanced Fluorine Biocatalysis br (2022)
CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability (2022)
Mechanism-Based Strategy for Optimizing HaloTag Protein Labeling (2022)
IMPACT OF ADMINISTRATION METHOD OF THROMBOLYTICS ON THEIR THROMBOLYTIC EFFECTS (2022)
DESIGN AND SYNTHESIS OF N-HYDROXY-CINNAMAMIDE DERIVATES AS NOVEL HDAC INHIBITORS: EVALUATION OF BIOLOGICAL ACTIVITY IN CANCER CELLS (2022)
sMolBoxes: Dataflow Model for Molecular Dynamics Exploration (2023)
Caver Web 1.2 (2022)
PredictSNP Onco 1.0 (2022)
SoluProtMutDB: A manually curated database of protein solubility changes upon mutations (2022)
Fully automated virtual screening pipeline of FDA-approved drugs using Caver Web (2022)
Structural Insights into (Tere)phthalate-Ester Hydrolysis by a Carboxylesterase and Its Role in Promoting PET Depolymerization (2022)
Virtual screening of potential anticancer drugs based on microbial products (2022)
Follistatin-like 1 and its paralogs in heart development and cardiovascular disease (2022)
Hidden Potential of Highly Efficient and Widely Accessible Thrombolytic Staphylokinase (2022)
Advanced database mining of efficient haloalkane dehalogenases by sequence and structure bioinformatics and microfluidics (2022)
Multiple Substrate Binding Mode-Guided Engineering of a Thermophilic PET Hydrolase (2022)
熱安定性ＦＧＦ２ポリペプチド及びその使用 (2022)
Nástroj LoopGrafter (2022)
Thermostable FGF2 polypeptide, use thereof (2023)
Catalytic mechanism for Renilla-type luciferases (2023)
Domino-like effect of C112R mutation on ApoE4 aggregation and its reduction by Alzheimer’s Disease drug candidate (2023)
Comparison of Fungal Thermophilic and Mesophilic Catalase-Peroxidases for Their Antioxidative Properties (2023)
Identification, characterization, and engineering of glycosylation in thrombolytics (2023)
pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support (2023)
Poměr plazminogen/plazmin jako ukazatel bezpečnosti trombolytické léčby (2023)
Advancing Enzyme's Stability and Catalytic Efficiency through Synergy of Force-Field Calculations, Evolutionary Analysis, and Machine Learning (2023)
InVADo: Interactive Visual Analysis of Molecular Docking Data (2024)
ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era (2024)
PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning (2024)
FireProt 2.0: web-based platform for the fully automated design of thermostable proteins (2024)
Thermostable FGF2 polypeptide, use thereof (2023)
Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum (2023)
Illuminating the mechanism and allosteric behavior of NanoLuc luciferase (2023)
Computer-assisted stabilization of fibroblast growth factor FGF-18 (2023)
Exploring new galaxies: Perspectives on the discovery of novel PET-degrading enzymes (2024)
Machine Learning-Guided Protein Engineering (2023)
Fully Automated Ancestral Sequence Reconstruction using FireProtASR (2021)
Computer-aided engineering of stabilized fibroblast growth factor 21 (2024)
Thermostable FGF2 Polypeptide, Use Thereof (2023)
Visual Support for the Loop Grafting Workflow on Proteins (2024)
A computational workflow for analysis of missense mutations in precision oncology (2024)
CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules (2024)
AggreProt: a web server for predicting and engineering aggregation prone regions in proteins (2024)
Azobenzene-Based Photoswitchable Substrates for Advanced Mechanistic Studies of Model Haloalkane Dehalogenase Enzyme Family (2024)
BenchStab: A tool for automated querying of web-based stability predictors (2024)
IDENTIFICATION OF NOVEL CYTOKININS BY MOLECULAR DOCKING (2024)
Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes (2024)

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