selected-publications

Selected Publications

Nemergut, M. et al. (2026)

Concentration-dependent dimerization of staphylokinase variants with engineered surface charges

Protein Science 35 (3): e70494. 

Jochymek, L. et al. (2026) 

GAN-based bone suppression using a combined loss function

Frontiers in Artificial Intelligence 9: 1761336.

Marques, S. et al. (2025)

Caver Web 2.0: analysis of tunnels and ligand transport in dynamic ensembles of proteins

Nucleic Acids Research 53: W132–W142.

 

Khan, R. et al. (2025)

Anticipating protein evolution with successor sequence predictor

Journal of Cheminformatics 17(1):34

 

Kohout, P. et al. (2025)

Engineering Dehalogenase Enzymes Using Variational Autoencoder-Generated Latent Spaces and Microfluidics 

JACS Au 5 :838-850. 

 

Planas-Iglesias, J. et al. (2025)

Automated Engineering Protein Dynamics via Loop Grafting: Improving Renilla Luciferase Catalysis

ACS Catalysis 15: 3391-3404.

 

Havlásek, M. et al. (2025)

Decoding Protein Stabilization: Impact on Aggregation, Solubility, and Unfolding Mechanisms

Journal of Chemical Information and Modeling 65 (16): 8688-8701. 

 

Štulajterová, M. et al. (2025)

Assessing the impact of His-tags on activity and stability of staphylokinase variants

International Journal of Biological Macromolecules 328: 147655. 

 

Franko, O. et al. (2025)

Acridine-Based Chalcone 1C and ABC Transporters

International Journal Of Molecular Sciences 26: 4138. 

 

Musil, M. et al. (2025)

FireProtDB 2.0: large-scale manually curated database of the protein stability data

Nucleic Acids Research 54: D409–D418. 

Phan, A. et al. (2025)

Refining the AOP for retinoid-induced teratogenicity: Insights into RAR/ RXR overactivation and RXR cross-talk with retinoic acid and thyroid hormone signaling

Aquatic Toxicology 289: 107608. 

 

Gregg, N.M. et al. (2025)

Thalamic Stimulation Induced Changes in Network Connectivity and Excitability in Epilepsy

Annals of Neurology 99:748–760. 

Buller, R. et al. (2024) 

Structure Prediction and Computational Protein Design for Efficient Biocatalysts and Bioactive Proteins 

Angewandte Chemie International Edition 64: e202421686. 

Maidenbaum, S. et al. (2025)

Improved spatial memory for physical versus virtual navigation

J. Neural Eng. 22: 046014. DOI 10.1088/1741-2552/ade6aa