David Bednář

Leakage-Controlled Benchmarking of Variant Effect Predictors and Development of Gradient-Boosting Consensus Model

The paper benchmarks variant effect predictors using a leakage-controlled dataset and develops a gradient-boosting consensus model that outperforms existing tools.

Uncovering Functional Distant Mutations by Ultra-High-Throughput Screening of Dehalogenases

This study uses ultrahigh-throughput screening to identify mutations in dehalogenases that modulate substrate access and binding, revealing distal functional effects on enzyme dynamics.

Multi-Objective Engineering of Fibrin-Selective Thrombolytic Proteases with Enhanced Biocatalytic Efficiency and Inhibition Resistance

This paper designs next-generation thrombolytic proteases with improved catalytic efficiency, fibrin selectivity, and inhibition resistance through multi-objective enzyme engineering.

Structural mechanism governing radiationless energy transfer in Renilla bioluminescence

This study reports co-crystal structures of a bioluminescent energy-transfer complex in Renilla reniformis, revealing the spatial arrangement of donor-acceptor chromophores and their role in efficient radiationless energy transfer.

Biochemical and Immunological Properties of Engineered Low-Immunogenic Staphylokinases for Next-Generation Thrombolytic Therapy

The paper compares biochemical and immunological properties of engineered low-immunogenic staphylokinase variants to identify the most promising for thrombolytic therapy.

ProtXAI: Explainable AI Reveals Structural Determinants of Protein Dynamics

ProtXAI combines molecular dynamics and explainable AI to identify residue-level determinants of protein conformational changes across diverse systems.

Taurine Inhibits Apolipoprotein E4 Aggregation

This study shows taurine inhibits ApoE4 aggregation and reduces its pathophysiological effects, similar to tramiprosate and 3-sulfopropanoic acid.

Investigating the Conformational Flexibility of Staphylokinase Across Multiple Time Scales

This study investigates the conformational flexibility of staphylokinase variants to explain their reduced immunogenicity and altered properties.

Molecular trick to reverse SN2 mechanism in hydrolytic enzyme

This paper shows that replacing histidine with phenylalanine in haloalkane dehalogenase reverses the SN2 mechanism by remodeling the active site, enabling reversible reactions for sustainable transhalogenation.

Conformational gating of product release sets the catalytic ceiling of a bioluminescent reporter

This study identifies conformational dynamics as a key determinant of luciferase catalytic efficiency and light-emission stability, revealing a trade-off between oxygen affinity and enzyme longevity.

Structural insights into the evolution of ABH-fold luciferases

This study determines the crystal structures and dynamical behavior of an ancestral ABH-fold enzyme, revealing molecular features that enabled the transition from hydrolytic to oxygenolytic catalysis.

Anticipating Protein Evolution with Successor Sequence Predictor

The paper introduces a computational method to predict protein evolution by reconstructing a protein's evolutionary history and suggesting future amino acid substitutions to improve desired properties.

Analysis of Mutations in Precision Oncology using The Automated, Accurate, and User-Friendly Web Tool PredictONCO

PredictONCO is a web tool that predicts the impact of mutations in cancer-related proteins using structural and sequence-based features, achieving high accuracy in variant classification.

Large-scale Annotation of Biochemically Relevant Pockets and Tunnels in Cognate Enzyme-Ligand Complexes

The paper develops a computational pipeline to annotate functional tunnels in enzyme-ligand complexes and validates it using molecular systems, showing it matches molecular dynamics simulations in speed and accuracy.

A Computational Workflow for Analysis of Missense Mutations in Precision Oncology

This paper presents a bioinformatics pipeline for analyzing missense mutations in oncogenic proteins, providing a probability score for functional impact and suggesting potential FDA/EMA-approved drugs.

Prediction of Aggregation Prone Regions in Proteins Using Deep Neural Networks and Their Suppression by Computational Design

This paper develops a deep neural network predictor, AggreProt, to identify aggregation-prone regions in proteins and demonstrates its utility in designing mutations to suppress aggregation.

Domino-like Effect of C112R Mutation on APOE4 Aggregation and Its Reduction by Alzheimer's Disease Drug Candidate

The paper investigates how the C112R mutation in ApoE4 causes aggregation and shows that tramiprosate reduces this aggregation.

A non-conventional archaeal fluorinase identified by in silico mining catalyzes the fastest natural nucleophilic fluorination

The paper identifies a novel archaeal fluorinase with the highest reported fluorination rate and demonstrates its application in enhancing fluoronucleotide production in bacterial hosts.

PepSeA: Peptide Sequence Alignment and Visualization Tools to Enable Lead Optimization

PepSeA provides tools for peptide sequence alignment and visualization to support lead optimization in drug discovery.