Jiřı́ Damborský

Research interests

Publications

• Machine Learning-Guided Protein Engineering

  ACS Catalysis · 2023 · 10.1021/acscatal.3c02743

• Mechanism-Based Design of Efficient PET Hydrolases

  ACS Catalysis · 2022 · 10.1021/acscatal.1c05856

• Multiple Substrate Binding Mode-Guided Engineering of a Thermophilic PET Hydrolase

  ACS Catalysis · 2022 · 10.1021/acscatal.2c02275

• SoluProt: prediction of soluble protein expression in Escherichia coli

  Bioinformatics · 2020 · 10.1093/bioinformatics/btaa1102

• Engineering enzyme access tunnels

  Biotechnology Advances · 2019 · 10.1016/j.biotechadv.2019.04.008

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

  Nucleic Acids Research · 2019 · 10.1093/nar/gkz378

• Machine Learning in Enzyme Engineering

  ACS Catalysis · 2019 · https://doi.org/10.1021/acscatal.9b04321

• Computational Design of Stable and Soluble Biocatalysts

  ACS Catalysis · 2018 · 10.1021/acscatal.8b03613

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

  Bioinformatics · 2018 · 10.1093/bioinformatics/bty386

• HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information

  Nucleic Acids Research · 2018 · 10.1093/nar/gky417

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

  Biotechnology Advances · 2017 · 10.1016/j.biotechadv.2017.08.001

• FireProt: web server for automated design of thermostable proteins

  Nucleic Acids Research · 2017 · 10.1093/nar/gkx285

• PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions

  PLoS Computational Biology · 2016 · 10.1371/journal.pcbi.1004962

• CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules

  IEEE Transactions on Computational Biology and Bioinformatics · 2015 · 10.1109/tcbb.2015.2459680

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

  PLoS Computational Biology · 2015 · 10.1371/journal.pcbi.1004556

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

  Microbial Cell Factories · 2015 · 10.1186/s12934-015-0393-3

• Computational tools for designing and engineering enzymes

  Current Opinion in Chemical Biology · 2014 · 10.1016/j.cbpa.2013.12.003

• PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

  PLoS Computational Biology · 2014 · https://doi.org/10.1371/journal.pcbi.1003440

• Strategies for Stabilization of Enzymes in Organic Solvents

  ACS Catalysis · 2013 · https://doi.org/10.1021/cs400684x

• Gates of Enzymes

  Chemical Reviews · 2013 · 10.1021/cr300384w

• CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

  PLoS Computational Biology · 2012 · https://doi.org/10.1371/journal.pcbi.1002708

• Haloalkane dehalogenases: Biotechnological applications

  Biotechnology Journal · 2012 · 10.1002/biot.201100486

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

  Nucleic Acids Research · 2009 · 10.1093/nar/gkp410

• Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate

  Nature Chemical Biology · 2009 · https://doi.org/10.1038/nchembio.205

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

  BMC Bioinformatics · 2006 · https://doi.org/10.1186/1471-2105-7-316

Current projects

No projects listed.