Jiří Damborský (Jiri Damborsky)

ResearcherID Loop profile ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 37

Top Topics

Crystal Structure

Machine Learning

Raman Spectroscopy

Top Venues

Nucleic acids research

Nature communications

This page only lists publications with an associated author ORCID identifier.

Publications

Sérgio M Marques, Petr Kouba, Anthony Legrand, Jiri Sedlar, Lucas Disson, Joan Planas-Iglesias, Zainab Sanusi, Antonin Kunka, Jiří Damborský, Tomas Pajdla, Zbynek Prokop, Stanislav Mazurenko, Josef Sivic, David Bednář
CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules. JACS Au 4 (6) (2024)
Joan Planas-Iglesias, Simeon Borko, Jan Swiatkowski, Matej Elias, Martin Havlasek, Ondrej Salamon, Ekaterina Grakova, Antonín Kunka, Tomas Martinovic, Jiří Damborský, Jan Martinovic, David Bednář
AggreProt: a web server for predicting and engineering aggregation prone regions in proteins. Nucleic acids research 52 (W1) (2024)
Sebastian Fruhauf, Dominic Pühringer, Michaela Thamhesl, Patricia Fajtl, Elisavet Kunz-Vekiru, Andreas Höbartner-Gussl, Gerd Schatzmayr, Gerhard Adam, Jiří Damborský, Kristina Djinovic-Carugo, Zbynek Prokop, Wulf-Dieter Moll
Bacterial Lactonases ZenA with Noncanonical Structural Features Hydrolyze the Mycotoxin Zearalenone. ACS catalysis 14 (5) (2024)
Sérgio M Marques, Petr Kouba, Anthony Legrand, Jiri Sedlar, Lucas Disson, Joan Planas-Iglesias, Zainab Sanusi, Antonin Kunka, Jiří Damborský, Tomas Pajdla, Zbynek Prokop, Stanislav Mazurenko, Josef Sivic, David Bednář
CoVAMPnet: Comparative Markov State Analysis for Studying Effects of Drug Candidates on Disordered Biomolecules. JACS Au 4 (6) (2024)
Joan Planas-Iglesias, Simeon Borko, Jan Swiatkowski, Matej Elias, Martin Havlasek, Ondrej Salamon, Ekaterina Grakova, Antonín Kunka, Tomas Martinovic, Jiří Damborský, Jan Martinovic, David Bednář
AggreProt: a web server for predicting and engineering aggregation prone regions in proteins. Nucleic acids research 52 (W1) (2024)
Sebastian Fruhauf, Dominic Pühringer, Michaela Thamhesl, Patricia Fajtl, Elisavet Kunz-Vekiru, Andreas Höbartner-Gussl, Gerd Schatzmayr, Gerhard Adam, Jiří Damborský, Kristina Djinovic-Carugo, Zbynek Prokop, Wulf-Dieter Moll
Bacterial Lactonases ZenA with Noncanonical Structural Features Hydrolyze the Mycotoxin Zearalenone. ACS catalysis 14 (5) (2024)
Joan Planas-Iglesias, Simeon Borko, Jan Swiatkowski, Matej Elias, Martin Havlasek, Ondrej Salamon, Ekaterina Grakova, Antonín Kunka, Tomas Martinovic, Jiří Damborský, Jan Martinovic, David Bednář
AggreProt: a web server for predicting and engineering aggregation prone regions in proteins. Nucleic acids research (2024)
Michaela Slanska, Lenka Stackova, Sergio M Marques, Peter Stacko, Marek Martínek, Luboš Jílek, Martin Toul, Jiří Damborský, David Bednar, Petr Klán, Zbynek Prokop
Azobenzene-Based Photoswitchable Substrates for Advanced Mechanistic Studies of Model Haloalkane Dehalogenase Enzyme Family. ACS catalysis 14 (15) (2024)
Michaela Slanska, Lenka Stackova, Sergio M Marques, Peter Stacko, Marek Martínek, Luboš Jílek, Martin Toul, Jiří Damborský, David Bednar, Petr Klán, Zbynek Prokop
Azobenzene-Based Photoswitchable Substrates for Advanced Mechanistic Studies of Model Haloalkane Dehalogenase Enzyme Family. ACS catalysis 14 (15) (2024)
Michal Nemergut, Daniel Pluskal, Jana Horackova, Tereza Sustrova, Jan Tulis, Tomas Barta, Racha Baatallah, Glwadys Gagnot, Veronika Novakova, Marika Majerova, Karolina Sedlackova, Sergio M Marques, Martin Toul, Jiří Damborský, Zbynek Prokop, David Bednář, Yves L Janin, Martin Marek
Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Nature communications 14 (1) (2023)
Petr Kouba, Pavel Kohout, Faraneh Haddadi, Anton Bushuiev, Raman Samusevich, Jiri Sedlar, Jiří Damborský, Tomáš Pluskal, Josef Sivic, Stanislav Mazurenko
Machine Learning-Guided Protein Engineering. ACS catalysis 13 (21) (2023)
Anna Špačková, Ondřej Vávra, Tomáš Raček, Václav Bazgier, David Sehnal, Jiří Damborský, Radka Svobodová, David Bednář, Karel Berka
ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era. Nucleic acids research (2023)
Milos Musil, Andrej Jezik, Jana Horackova, Simeon Borko, Petr Kabourek, Jiří Damborský, David Bednář
FireProt 2.0: web-based platform for the fully automated design of thermostable proteins. Briefings in bioinformatics 25 (1) (2023)
Antonin Kunka, Sergio M Marques, Martin Havlasek, Michal Vasina, Nikola Velatova, Lucia Cengelova, David Kovář, Jiří Damborský, Martin Marek, David Bednar, Zbynek Prokop
Advancing Enzyme's Stability and Catalytic Efficiency through Synergy of Force-Field Calculations, Evolutionary Analysis, and Machine Learning. ACS catalysis 13 (19) (2023)
Martin Toul, Jan Mican, Veronika Slonkova, Dmitri Nikitin, Martin Marek, David Bednář, Jiří Damborský, Zbynek Prokop
Hidden Potential of Highly Efficient and Widely Accessible Thrombolytic Staphylokinase. Stroke 53 (10) (2022)
Sergio M Marques, Michaela Slanska, Klaudia Chmelova, Radka Chaloupkova, Martin Marek, Spencer Clark, Jiří Damborský, Eric T Kool, David Bednar, Zbynek Prokop
Mechanism-Based Strategy for Optimizing HaloTag Protein Labeling. JACS Au 2 (6) (2022)
Antonin Kunka, David Lacko, Jan Stourac, Jiří Damborský, Zbynek Prokop, Stanislav Mazurenko
CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability. Nucleic acids research (2022)
Jakub Pospíšil, Miloš Hrabovský, Dáša Bohačiaková, Zuzana Hovádková, Miroslav Jurásek, Jarmila Mlčoušková, Kamil Paruch, Šárka Nevolová, Jiří Damborský, Aleš Hampl, Josef Jaros
Geometric Control of Cell Behavior by Biomolecule Nanodistribution. ACS biomaterials science & engineering 8 (11) (2022)
Joan Planas-Iglesias, Filip Opaleny, Pavol Ulbrich, Jan Stourac, Zainab Sanusi, Gaspar P Pinto, Andrea Schenkmayerova, Jan Byska, Jiří Damborský, Barbora Kozlikova, David Bednář
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. Nucleic acids research (2022)
Andrea Schenkmayerova, Gaspar P Pinto, Martin Toul, Martin Marek, Lenka Hernychova, Joan Planas-Iglesias, Veronika Daniel Liskova, Daniel Pluskal, Michal Vasina, Stephane Emond, Mark Dörr, Radka Chaloupkova, David Bednar, Zbynek Prokop, Florian Hollfelder, Uwe T Bornscheuer, Jiří Damborský
Engineering the protein dynamics of an ancestral luciferase. Nature communications 12 (1) (2021)
Andrii Mazur, Pavel Grinkevich, Radka Chaloupkova, Petra Havlickova, Barbora Kascakova, Michal Kuty, Jiří Damborský, Ivana Kuta Smatanova, Tatyana Prudnikova
Structural Analysis of the Ancestral Haloalkane Dehalogenase AncLinB-DmbA. International journal of molecular sciences 22 (21) (2021)
Piia Kokkonen, Andy Beier, Stanislav Mazurenko, Jiří Damborský, David Bednář, Zbynek Prokop
Substrate inhibition by the blockage of product release and its control by tunnel engineering. RSC chemical biology 2 (2) (2021)
Dana Vigasova, Michal Nemergut, Barbora Liskova, Jiří Damborský
Multi-pathogen infections and Alzheimer's disease. Microbial cell factories 20 (1) (2021)
Klaudia Chmelova, Eva Sebestova, Veronika Liskova, Andy Beier, David Bednar, Zbynek Prokop, Radka Chaloupkova, Jiří Damborský
A Haloalkane Dehalogenase from Saccharomonospora viridis Strain DSM 43017, a Compost Bacterium with Unusual Catalytic Residues, Unique (S)-Enantiopreference, and High Thermostability. Applied and environmental microbiology 86 (17) (2020)
Aşkın S Aslan-Üzel, Andy Beier, David Kovář, Clemens Cziegler, Santosh K Padhi, Eva D Schuiten, Mark Dörr, Dominique Böttcher, Frank Hollmann, Florian Rudroff, Marko D Mihovilovic, Tomáš Buryška, Jiří Damborský, Zbynek Prokop, Christoffel P S Badenhorst, Uwe T Bornscheuer
An Ultrasensitive Fluorescence Assay for the Detection of Halides and Enzymatic Dehalogenation. ChemCatChem 12 (7) (2020)
Klara Markova, Klaudia Chmelova, Sérgio M Marques, Philippe Carpentier, David Bednar, Jiří Damborský, Martin Marek
Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst. Chemical science 11 (41) (2020)
Katsiaryna Tratsiak, Tatyana Prudnikova, Ivana Drienovska, Jiří Damborský, Jiri Brynda, Petr Pachl, Michal Kuty, Radka Chaloupkova, Pavlína Řezáčová, Ivana Kuta Smatanova
Crystal structure of the cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5. Acta crystallographica. Section F, Structural biology communications 75 (Pt 5) (2019)
Martin Demko, Lukáš Chrást, Pavel Dvořák, Jiří Damborský, David Šafránek
Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway. Microorganisms 7 (11) (2019)
Tomas Buryska, Michal Vasina, Fabrice Gielen, Pavel Vanacek, Liisa van Vliet, Jan Jezek, Zdenek Pilat, Pavel Zemanek, Jiří Damborský, Florian Hollfelder, Zbynek Prokop
Controlled Oil/Water Partitioning of Hydrophobic Substrates Extending the Bioanalytical Applications of Droplet-Based Microfluidics. Analytical chemistry 91 (15) (2019)
Pavel Dvorak, David Bednar, Pavel Vanacek, Lukas Balek, Livia Eiselleova, Veronika Stepankova, Eva Sebestova, Michaela Kunova Bosakova, Zaneta Konecna, Stanislav Mazurenko, Antonin Kunka, Tereza Vanova, Karolina Zoufalova, Radka Chaloupkova, Jan Brezovsky, Pavel Krejci, Zbynek Prokop, Petr Dvorak, Jiří Damborský
Computer-assisted engineering of hyperstable fibroblast growth factor 2. Biotechnology and bioengineering 115 (4) (2018)
Zdenek Pilat, Martin Kizovský, Jan Ježek, Stanislav Krátký, Jaroslav Sobota, Martin Šiler, Ota Samek, Tomáš Buryška, Pavel Vaňáček, Jiří Damborský, Zbyněk Prokop, Pavel Zemánek
Detection of Chloroalkanes by Surface-Enhanced Raman Spectroscopy in Microfluidic Chips. Sensors (Basel, Switzerland) 18 (10) (2018)
Shubhangi Kaushik, Sérgio M Marques, Prashant Khirsariya, Kamil Paruch, Lenka Libichova, Jan Brezovsky, Zbynek Prokop, Radka Chaloupkova, Jiří Damborský
Impact of the access tunnel engineering on catalysis is strictly ligand-specific. The FEBS journal 285 (8) (2018)
Piia Kokkonen, Jan Sykora, Zbynek Prokop, Avisek Ghose, David Bednar, Mariana Amaro, Koen Beerens, Sarka Bidmanova, Michaela Slanska, Jan Brezovsky, Jiří Damborský, Martin Hof
Molecular Gating of an Engineered Enzyme Captured in Real Time. Journal of the American Chemical Society 140 (51) (2018)
Michael Kotik, Pavel Vanacek, Antonin Kunka, Zbynek Prokop, Jiří Damborský
Metagenome-derived haloalkane dehalogenases with novel catalytic properties. Applied microbiology and biotechnology 101 (16) (2017)
Veronika Liskova, Veronika Stepankova, David Bednar, Jan Brezovsky, Zbynek Prokop, Radka Chaloupkova, Jiří Damborský
Different Structural Origins of the Enantioselectivity of Haloalkane Dehalogenases toward Linear β-Haloalkanes: Open-Solvated versus Occluded-Desolvated Active Sites. Angewandte Chemie (International ed. in English) 56 (17) (2017)
Stanislav Mazurenko, Antonin Kunka, Koen Beerens, Christopher M Johnson, Jiří Damborský, Zbynek Prokop
Exploration of Protein Unfolding by Modelling Calorimetry Data from Reheating. Scientific reports 7 (1) (2017)
Sérgio M Marques, Zuzana Dunajova, Zbynek Prokop, Radka Chaloupkova, Jan Brezovsky, Jiří Damborský
Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling. Journal of chemical information and modeling 57 (8) (2017)