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Scopus Author ID: 56374157300

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Employment (2)

Masaryk University: Brno, CZ

2017-06-01 to present | Team Leader (Department of Experimental Biology)
Employment
Source: Self-asserted source
David Bednar

Enantis (Czechia): Brno, CZ

2017-01-01 to present | Research consultant
Employment
Source: Self-asserted source
David Bednar

Education and qualifications (1)

Masaryk University: Brno, CZ

2011-08-01 to 2017-04-21 | Ph.D. (Department of Experimental Biology)
Education
Source: Self-asserted source
David Bednar

Works (37)

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

ACS Catalysis
2025-02-21 | Journal article
DOI: 10.1021/acscatal.4c06207
Contributors: Joan Planas-Iglesias; Marika Majerova; Daniel Pluskal; Michal Vasina; Jiri Damborsky; Zbynek Prokop; Martin Marek; David Bednar
Source: check_circle
Crossref

Visual Support for the Loop Grafting Workflow on Proteins

IEEE Transactions on Visualization and Computer Graphics
2025-01 | Journal article
DOI: 10.1109/TVCG.2024.3456401
Contributors: Filip Opálený; Pavol Ulbrich; Joan Planas-Iglesias; Jan Byška; Jan Štourač; David Bednář; Katarína Furmanová; Barbora Kozlíková
Source: check_circle
Crossref

Accelerating Enzyme Engineering with Quantum Power: Quest for Quantum Advantage in Biocatalysis

2024-11-19 | Preprint
DOI: 10.26434/chemrxiv-2024-pwkq5
Contributors: Jiri Damborsky; Petr Kouba; Josef Sivic; David Bednar; Stanislav Mazurenko
Source: check_circle
Crossref

BenchStab: a tool for automated querying of web-based stability predictors

Bioinformatics
2024-09-02 | Journal article
DOI: 10.1093/bioinformatics/btae553
Contributors: Jan Velecký; Matej Berezný; Milos Musil; Jiri Damborsky; David Bednar; Stanislav Mazurenko; Macha Nikolski
Source: check_circle
Crossref

InVADo: Interactive Visual Analysis of Molecular Docking Data

IEEE Transactions on Visualization and Computer Graphics
2024-04 | Journal article
DOI: 10.1109/TVCG.2023.3337642
Contributors: Marco Schäfer; Nicolas Brich; Jan Byška; Sérgio M. Marques; David Bednář; Philipp Thiel; Barbora Kozlíková; Michael Krone
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Crossref

Exploring new galaxies: Perspectives on the discovery of novel PET-degrading enzymes

Applied Catalysis B: Environmental
2024-03 | Journal article
DOI: 10.1016/j.apcatb.2023.123404
Contributors: Jan Mican; Da'san M.M. Jaradat; Weidong Liu; Gert Weber; Stanislav Mazurenko; Uwe T. Bornscheuer; Jiri Damborsky; Ren Wei; David Bednar
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Crossref

ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era

Nucleic Acids Research
2024-01-05 | Journal article
DOI: 10.1093/nar/gkad1012
Contributors: Anna Špačková; Ondřej Vávra; Tomáš Raček; Václav Bazgier; David Sehnal; Jiří Damborský; Radka Svobodová; David Bednář; Karel Berka
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Crossref

FireProt 2.0: web-based platform for the fully automated design of thermostable proteins

Briefings in Bioinformatics
2023-11-22 | Journal article
DOI: 10.1093/bib/bbad425
Contributors: Milos Musil; Andrej Jezik; Jana Horackova; Simeon Borko; Petr Kabourek; Jiri Damborsky; David Bednar
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Crossref

Atypical homodimerization revealed by the structure of the (S)-enantioselective haloalkane dehalogenase DmmarA from Mycobacterium marinum

Acta Crystallographica Section D Structural Biology
2023-11-01 | Journal article
DOI: 10.1107/S2059798323006642
Contributors: Karolina Snajdarova; Sérgio M. Marques; Jiri Damborsky; David Bednar; Martin Marek
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Crossref

pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support

Bioinformatics
2023-08-01 | Journal article
DOI: 10.1093/bioinformatics/btad443
Contributors: Ondrej Vavra; Jakub Beranek; Jan Stourac; Martin Surkovsky; Jiri Filipovic; Jiri Damborsky; Jan Martinovic; David Bednar; Alfonso Valencia
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Crossref

Hidden Potential of Highly Efficient and Widely Accessible Thrombolytic Staphylokinase

Stroke
2022-10 | Journal article
DOI: 10.1161/STROKEAHA.122.040219
Contributors: Martin Toul; Jan Mican; Veronika Slonkova; Dmitri Nikitin; Martin Marek; David Bednar; Jiri Damborsky; Zbynek Prokop
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Crossref

Deep Insights into the Specific Evolution of Fungal Hybrid B Heme Peroxidases

Biology
2022-03 | Journal article | Author
DOI: 10.3390/biology11030459
Contributors: Marcel Zamocky; Milos Musil; Maksym Danchenko; Peter Ferianc; Katarína Chovanová; Peter Barath; Andrej Poljovka; David Bednar
Source: check_circle
Multidisciplinary Digital Publishing Institute
grade
Preferred source (of 2)‎

Substrate inhibition by the blockage of product release and its control by tunnel engineering

RSC Chemical Biology
2021 | Journal article
DOI: 10.1039/D0CB00171F
Contributors: Piia Kokkonen; Andy Beier; Stanislav Mazurenko; Jiri Damborsky; David Bednar; Zbynek Prokop
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Crossref

Screening of Natural Compounds as P-Glycoprotein Inhibitors against Multidrug Resistance

Biomedicines
2021-03-30 | Journal article
DOI: 10.3390/biomedicines9040357
Contributors: Sérgio M. Marques; Lucie Šupolíková; Lenka Molčanová; Karel Šmejkal; David Bednar; Iva Slaninová
Source: check_circle
Crossref

Virtual Screening of Potential Anticancer Drugs based on Microbial Products

2021-02-23 | Other
DOI: 10.20944/preprints202102.0529.v1
Contributors: Gaspar Pinto; Natalie Hendrikse; Jan Stourac; Jiri Damborsky; David Bednar
Source: check_circle
Crossref

FireProtDB: database of manually curated protein stability data

Nucleic Acids Research
2021-01-08 | Journal article
DOI: 10.1093/nar/gkaa981
Contributors: Jan Stourac; Juraj Dubrava; Milos Musil; Jana Horackova; Jiri Damborsky; Stanislav Mazurenko; David Bednar
Source: check_circle
Crossref

EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities

Nucleic Acids Research
2020-07-02 | Journal article
DOI: 10.1093/nar/gkaa372
Contributors: Jiri Hon; Simeon Borko; Jan Stourac; Zbynek Prokop; Jaroslav Zendulka; David Bednar; Tomas Martinek; Jiri Damborsky
Source: check_circle
Crossref

CaverDock: A Novel Method for the Fast Analysis of Ligand Transport

IEEE/ACM Transactions on Computational Biology and Bioinformatics
2019 | Journal article
DOI: 10.1109/tcbb.2019.2907492
Part of ISSN: 1545-5963
Part of ISSN: 1557-9964
Part of ISSN: 2374-0043
Source: Self-asserted source
David Bednar

Structural Biology and Protein Engineering of Thrombolytics

Computational and Structural Biotechnology Journal
2019 | Journal article
DOI: 10.1016/j.csbj.2019.06.023
Part of ISSN: 2001-0370
Source: Self-asserted source
David Bednar

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

Nucleic Acids Research
2019-07-02 | Journal article
DOI: 10.1093/nar/gkz378
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962
Source: Self-asserted source
David Bednar

CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels

Bioinformatics
2019-05-11 | Journal article
DOI: 10.1093/bioinformatics/btz386
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Source: Self-asserted source
David Bednar

Engineering enzyme access tunnels

Biotechnology Advances
2019-04 | Journal article
DOI: 10.1016/j.biotechadv.2019.04.008
Part of ISSN: 0734-9750
Source: Self-asserted source
David Bednar

Computational Design of Stable and Soluble Biocatalysts

ACS Catalysis
2019-02 | Journal article
DOI: 10.1021/acscatal.8b03613
Part of ISSN: 2155-5435
Part of ISSN: 2155-5435
Source: Self-asserted source
David Bednar

Computational Study of Protein-Ligand Unbinding for Enzyme Engineering

Frontiers in Chemistry
2019-01-08 | Journal article
DOI: 10.3389/fchem.2018.00650
Part of ISSN: 2296-2646
Source: Self-asserted source
David Bednar

Molecular Gating of an Engineered Enzyme Captured in Real Time

Journal of the American Chemical Society
2018-12-26 | Journal article
DOI: 10.1021/jacs.8b09848
Part of ISSN: 0002-7863
Part of ISSN: 1520-5126
Source: Self-asserted source
David Bednar
grade
Preferred source (of 2)‎

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

Bioinformatics
2018-10-15 | Journal article
DOI: 10.1093/bioinformatics/bty386
Part of ISSN: 1367-4803
Part of ISSN: 1460-2059
Source: Self-asserted source
David Bednar

Evolutionary Analysis As a Powerful Complement to Energy Calculations for Protein Stabilization

ACS Catalysis
2018-10-05 | Journal article
DOI: 10.1021/acscatal.8b01677
Part of ISSN: 2155-5435
Part of ISSN: 2155-5435
Source: Self-asserted source
David Bednar

Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site

Journal of Biological Chemistry
2018-07-20 | Journal article
DOI: 10.1074/jbc.ra117.000328
Part of ISSN: 0021-9258
Part of ISSN: 1083-351X
Source: Self-asserted source
David Bednar

CalFitter: a web server for analysis of protein thermal denaturation data

Nucleic Acids Research
2018-07-02 | Journal article
DOI: 10.1093/nar/gky358
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962
Source: Self-asserted source
David Bednar

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

Nucleic Acids Research
2018-07-02 | Journal article
DOI: 10.1093/nar/gky417
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962
Source: Self-asserted source
David Bednar

Computer‐assisted engineering of hyperstable fibroblast growth factor 2

Biotechnology and Bioengineering
2018-04 | Journal article
DOI: 10.1002/bit.26531
Part of ISSN: 0006-3592
Part of ISSN: 1097-0290
Source: Self-asserted source
David Bednar

FireProt: web server for automated design of thermostable proteins

Nucleic Acids Research
2017-07-03 | Journal article
DOI: 10.1093/nar/gkx285
Part of ISSN: 0305-1048
Part of ISSN: 1362-4962
Source: Self-asserted source
David Bednar

Different Structural Origins of the Enantioselectivity of Haloalkane Dehalogenases toward Linear β-Haloalkanes: Open-Solvated versus Occluded-Desolvated Active Sites

Angewandte Chemie International Edition
2017-04-18 | Journal article
DOI: 10.1002/anie.201611193
Part of ISSN: 1433-7851
Source: Self-asserted source
David Bednar

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

PLOS Computational Biology
2015-11-03 | Journal article
DOI: 10.1371/journal.pcbi.1004556
Part of ISSN: 1553-7358
Source: Self-asserted source
David Bednar

Site-Specific Analysis of Protein Hydration Based on Unnatural Amino Acid Fluorescence

Journal of the American Chemical Society
2015-04-22 | Journal article
DOI: 10.1021/jacs.5b01681
Part of ISSN: 0002-7863
Part of ISSN: 1520-5126
Source: Self-asserted source
David Bednar

Balancing the Stability-Activity Trade-Off by Fine-Tuning Dehalogenase Access Tunnels

ChemCatChem
2015-02 | Journal article
DOI: 10.1002/cctc.201402792
Part of ISSN: 1867-3880
Source: Self-asserted source
David Bednar

CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures

Bioinformatics
2014-09-15 | Journal article
DOI: 10.1093/bioinformatics/btu364
Part of ISSN: 1460-2059
Part of ISSN: 1367-4803
Source: Self-asserted source
David Bednar
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