Results

Hernández-Arriaga AM, Campano C, Rivero-Buceta V, Prieto MA. 2022. When microbial biotechnology meets material engineering. Microbial Biotechnology, https://doi.org/10.1111/1751-7915.13975

Vigasova D, Nemergut M, Liskova B, Damborsky J. 2021 Multi-pathogen infections and Alzheimer's disease. Microbial Cell Factories, https://doi.org/10.1186/s12934-021-01520-7

Khan RT, Musil M, Stourac J, Damborsky J, Bednar D. 2021. Fully Automated Ancestral Sequence Reconstruction using FireProtASR. Current Protocols, https://doi.org/10.1002/cpz1.30

Orsi E, Claassens NJ, Nikel PI, Lindner SN. 2021. Growth-coupled selection of synthetic modules to accelerate cell factory development. Nature Communications, https://doi.org/10.1038/s41467-021-25665-6

Griffith CM, Walvekar AS, Linster CL. 2021. Approaches for completing metabolic networks through metabolite damage and repair discovery. Current Opinion in Systems Biology, https://doi.org/10.1016/j.coisb.2021.100379

Cros A, Alfaro-Espinoza G, De Maria A, Wirth NT, Nikel PI. 2021. Synthetic metabolism for biohalogenation. Current Opinion in Biotechnology, https://doi.org/10.1016/j.copbio.2021.11.009

Marques SM, Planas-Iglesias J, Damborsky J. 2021. Web-based tools for computational enzyme design. Current Opinion in Structural Biology, https://doi.org/10.1016/j.sbi.2021.01.010

Musil M, Khan RT, Beier A, Stourac J, Konegger H, Damborsky J, Bednar D. 2021. FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction. Briefings in Bioinformatics, https://doi.org/10.1093/bib/bbaa337

Hon J, Marusiak M, Martinek T, Kunka A, Zendulka J, Bednar D, Damborsky J. 2021. SoluProt: Prediction of Soluble Protein Expression in Escherichia coli. Bioinformatics, https://doi.org/10.1093/bioinformatics/btaa1102

Markova K, Kunka A, Chmelova K, Havlasek M, Babkova P, Marques SM, Vasina M, Planas-Iglesias J, Chaloupkova R, Bednar D, Prokop Z, Damborsky J, and Marek M. 2021. Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers. ACS Catalysis, https://doi.org/10.1021/acscatal.1c03343

Pinto GP, Vavra O, Marques SM, Filipovic J, Bednar D, Damborsky J. 2021. Screening of world approved drugs against highly dynamical spike glycoprotein of SARS-CoV-2 using CaverDock and machine learning. Computational and Structural Biotechnology Journal, https://doi.org/10.1016/j.csbj.2021.05.043

Pérez-Pantoja D, Nikel PI, Chavarría M, de Lorenzo V. 2021. Transcriptional control of 2,4-dinitrotoluene degradation in Burkholderia sp. R34 bears a regulatory patch that eases pathway evolution. Environmental Microbiology, https://doi.org/10.1111/1462-2920.15472

Mezzina MP, Manoli MT, Prieto MA, Nikel Pl. 2020. Engineering Native and Synthetic Pathways in Pseudomonas putida for the Production of Tailored Polyhydroxyalkanoates. Biotechnology Journal, https://doi.org/10.1002/biot.202000165

Lammens EM, Nikel PI, Lavigne R. 2020. Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria. Nature Communications, https://doi.org/10.1038/s41467-020-19124-x

Dockalova V, Sanchez-Carnerero EM, Dunajova Z, Palao E, Slanska M, Buryska T, Damborsky J, Klán P, Prokop Z. 2020. Fluorescent substrates for haloalkane dehalogenases: Novel probes for mechanistic studies and protein labeling. Computational and Structural Biotechnology Journal, https://doi.org/10.1016/j.csbj.2020.03.029

Nieto-Domínguez M, Nikel PI. Markova K, Chmelova K, Marques SM, Carpentier P, Bednar D, Damborsky J, Marek M. 2020. Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst. Chemical Science, https://doi.org/10.1039/D0SC03367G

Marek M, Chaloupkova R, Prudnikova T, Sato Y, Rezacova P, Nagata Y, Kuta Smatanova I, Damborsky J. 2020. Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family. Computational and Structural Biotechnology Journal, https://doi.org/10.1016/j.csbj.2020.05.019

Chmelova K, Sebestova E, Liskova V, Beier A, Bednar D, Prokop Z, Chaloupkova R, Damborsky J. A 2020. 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, https://doi.org/10.1128/AEM.02820-19

Markakis K, Lowe PT, Davison-Gates L, O'Hagan D, Rosser SJ, Elfick A. 2020. An Engineered E. coli Strain for Direct in Vivo Fluorination. ChemBioChem, https://doi.org/10.1002/cbic.202000051

Calero P, Volke DC, Lowe PT et al. 2020. A fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida. Nature Communications, https://doi.org/10.1038/s41467-020-18813-x

Nieto-Domínguez M, Nikel PI. 2020. Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life. ChemBioChem, https://doi.org/10.1002/cbic.202000091

Babkova P, Dunajova Z, Chaloupkova R, Damborsky J, Bednar D, Marek M. 2020. Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics. Computational and Structural Biotechnology Journal, https://doi.org/10.1016/j.csbj.2020.06.021

Vavra O, Filipovic J, Plhak J, Bednar D, Marques SM, Brezovsky J, Stourac J, Matyska L, Damborsky J. 2019. CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinformatics, https://doi.org/10.1093/bioinformatics/btz386

Beier A, Damborsky J, Prokop Z. 2019. Transhalogenation Catalysed by Haloalkane Dehalogenases Engineered to Stop Natural Pathway at Intermediate. Advanced Synthesis and Catalysis, https://doi.org/10.1128/AEM.02820-19

Arce‐Rodríguez A, Volke DC,  Bense S,  Häussler S,  Nike PI. 2019. Non‐invasive, ratiometric determination of intracellular pH in Pseudomonas species using a novel genetically encoded indicator. Microbial Biotechnology Vol.12(4): 799-813. https://doi.org/10.1111/1751-7915.13439

Fernández‐Cabezón L., Cros A., and Nikel PI. 2019. Evolutionary Approaches for Engineering Industrially Relevant Phenotypes in Bacterial Cell Factories. Biotechnology Journal. https://doi.org/10.1002/biot.201800439

Martinelli L, Nikel PI. 2019. Breaking the state‐of‐the‐art in the chemical industry with new‐to‐Nature products via synthetic microbiology. Microbial Biotechnology. Vol. 12(2): 187-190. https://doi.org/10.1111/1751-7915.13372