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Jiri Damborsky

Jiri Damborsky

D-Index & Metrics

Chemistry

D-Index
71
Citations
17576
World Ranking
5571
National Ranking
25

Overview

Jiri Damborsky is affiliated with Masaryk University in the Czech Republic and has an extensive research record predominantly in the field of Biochemistry, Genetics, and Molecular Biology. Their work focuses heavily on Molecular Biology, with additional contributions to Materials Chemistry, Biomedical Engineering, Computational Theory and Mathematics, and Physiology.

The scientist's research covers a range of topics centered on protein science and computational biology. These include:

  • Protein Structure and Dynamics
  • Enzyme Structure and Function
  • Microbial Metabolic Engineering and Bioproduction
  • Enzyme Catalysis and Immobilization
  • Computational Drug Discovery Methods
  • Bioluminescence and Chemiluminescence Research
  • Bioinformatics and Genomic Networks

Jiri Damborsky has frequently published in several scientific venues, with a notable number of articles in:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • ACS Catalysis
  • Computational and Structural Biotechnology Journal
  • Nucleic Acids Research
  • Zenodo (CERN European Organization for Nuclear Research)

Their recent publications include:

  • "Mechanism-Based Design of Efficient PET Hydrolases," 2022, ACS Catalysis
  • "SoluProt: prediction of soluble protein expression in Escherichia coli," 2020, Bioinformatics
  • "Multiple Substrate Binding Mode-Guided Engineering of a Thermophilic PET Hydrolase," 2022, ACS Catalysis
  • "Machine Learning-Guided Protein Engineering," 2023, ACS Catalysis
  • "FireProtDB: database of manually curated protein stability data," 2020, Nucleic Acids Research

Among frequent collaborators are several researchers who have coauthored numerous publications with Jiri Damborsky. These coauthors include:

  • David Bednář
  • Zbyněk Prokop
  • Martin Marek
  • Stanislav Mazurenko
  • Sérgio M. Marques

Best Publications

  • CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.

    Eva Chovancova;Antonin Pavelka;Petr Benes;Ondrej Strnad

  • Strategies for Stabilization of Enzymes in Organic Solvents

    Veronika Stepankova;Sarka Bidmanova;Tana Koudelakova;Zbynek Prokop

  • CAVER: a new tool to explore routes from protein clefts, pockets and cavities

    Martin Petřek;Michal Otyepka;Pavel Banáš;Pavlína Košinová

  • CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories.

    Adam Jurcik;David Bednar;Jan Byska;Sergio M Marques

  • Machine Learning in Enzyme Engineering

    Stanislav Mazurenko;Zbynek Prokop;Zbynek Prokop;Jiri Damborsky;Jiri Damborsky

  • Redesigning Dehalogenase Access Tunnels as a Strategy for Degrading an Anthropogenic Substrate.

    Martina Pavlova;Martin Klvana;Zbynek Prokop;Radka Chaloupkova

  • Bioremediation 3.0: Engineering pollutant-removing bacteria in the times of systemic biology.

    Pavel Dvořák;Pablo Ivan Nikel;Jiří Damborský;Victor de Lorenzo

  • Gates of enzymes.

    Artur Gora;Jan Brezovsky;Jiri Damborsky

  • Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport

    Jan Stourac;Ondrej Vavra;Piia Kokkonen;Jiri Filipovic

  • Exacerbation of substrate toxicity by IPTG in Escherichia coli BL21(DE3) carrying a synthetic metabolic pathway

    Pavel Dvorak;Lukas Chrast;Pablo I. Nikel;Radek Fedr

  • Mechanism-Based Design of Efficient PET Hydrolases

    Unknown

  • HotSpot Wizard: a web server for identification of hot spots in protein engineering

    Antonin Pavelka;Eva Chovancova;Jiri Damborsky

  • Computational tools for designing and engineering enzymes.

    Jiri Damborsky;Jan Brezovsky

  • Engineering enzyme access tunnels.

    Piia Kokkonen;David Bednar;Gaspar Pinto;Zbynek Prokop

  • SoluProt: Prediction of Soluble Protein Expression in Escherichia coli.

    Jiri Hon;Martin Marusiak;Tomas Martinek;Antonin Kunka

  • Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel

    Radka Chaloupková;Jana Sýkorová;Zbyňek Prokop;Andrea Jesenská

  • FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants.

    David Bednar;Koen Beerens;Eva Sebestova;Jaroslav Bendl

  • Purification and characterization of a haloalkane dehalogenase of a new substrate class from a gamma-hexachlorocyclohexane-degrading bacterium, Sphingomonas paucimobilis UT26.

    Yuji Nagata;Keisuke Miyauchi;Jiri Damborsky;Katka Manova

  • Biodegradation of 1,2,3-trichloropropane through directed evolution and heterologous expression of a haloalkane dehalogenase gene

    Tjibbe Bosma;Jirí Damborský;Gerhard Stucki;Dick B. Janssen

  • Haloalkane dehalogenases: biotechnological applications.

    Tana Koudelakova;Sarka Bidmanova;Pavel Dvorak;Antonin Pavelka

  • Crystal Structure of the Haloalkane Dehalogenase from Sphingomonas paucimobilis UT26

    J Marek;J Vevodova;I.K Smatanova;I.K Smatanova;Y Nagata

  • Engineering enzyme stability and resistance to an organic cosolvent by modification of residues in the access tunnel

    Tana Koudelakova;Radka Chaloupkova;Jan Brezovsky;Zbynek Prokop

  • CAVER: algorithms for analyzing dynamics of tunnels in macromolecules

    Antonin Pavelka;Eva Sebestova;Barbora Kozlikova;Jan Brezovsky

  • Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering

    Zbynek Prokop;Yukari Sato;Jan Brezovsky;Tomas Mozga

  • Catalytic mechanism of the haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26

    Zbyněk Prokop;Marta Monincová;Radka Chaloupková;Martin Klvaňa

  • Substrate Specificity of Haloalkane Dehalogenases

    Tana Koudelakova;Eva Chovancova;Jan Brezovsky;Marta Monincova

  • Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored Using Classical and Random Acceleration Molecular Dynamics Simulations

    Martin Klvana;Martina Pavlova;Tana Koudelakova;Radka Chaloupkova

Frequent Co-Authors

Yuji Nagata
Yuji Nagata Tohoku University
Uwe T. Bornscheuer
Uwe T. Bornscheuer University of Greifswald
Masataka Tsuda
Masataka Tsuda Tohoku University
Florian Hollfelder
Florian Hollfelder University of Cambridge
Lumir Krejci
Lumir Krejci Masaryk University
Masahiro Takagi
Masahiro Takagi Kyoto Sangyo University
Ivan Rychlik
Ivan Rychlik Veterinary Research Institute
Rup Lal
Rup Lal University of Delhi
Martin Hof
Martin Hof Czech Academy of Sciences
Lenka Foretova
Lenka Foretova Masaryk University

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