David Bednar

According to our database, David Bednar authored at least 26 papers between 2011 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes.

Ondrej Vavra, Jonathan D. Tyzack, Farzan Haddadi, Jan Stourac, Jirí Damborský, Stanislav Mazurenko, Janet M. Thornton, David Bednar

J. Cheminformatics, December, 2024

A computational workflow for analysis of missense mutations in precision oncology.

Rayyan T. Khan, Petra Pokorna, Jan Stourac, Simeon Borko, Ihor Arefiev, Joan Planas-Iglesias, Adam Dobias, Gaspar R. P. Pinto, Veronika Szotkowska, Jaroslav Sterba, Ondrej Slaby, Jirí Damborský, Stanislav Mazurenko, David Bednar

J. Cheminformatics, December, 2024

InVADo: Interactive Visual Analysis of Molecular Docking Data.

Marco Schäfer, Nicolas Brich, Jan Byska, Sérgio M. Marques, David Bednár, Philipp Thiel, Barbora Kozlíková, Michael Krone

IEEE Trans. Vis. Comput. Graph., April, 2024

Visual Support for the Loop Grafting Workflow on Proteins.

Filip Opálený, Pavol Ulbrich, Joan Planas-Iglesias, Jan Byska, Jan Stourac, David Bednár, Katarína Furmanová, Barbora Kozlíková

CoRR, 2024

2023

PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning.

Jan Stourac, Simeon Borko, Rayyan T. Khan, Petra Pokorna, Adam Dobias, Joan Planas-Iglesias, Stanislav Mazurenko, Gaspar R. P. Pinto, Veronika Szotkowska, Jaroslav Sterba, Ondrej Slaby, Jirí Damborský, David Bednar

Briefings Bioinform., November, 2023

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

Milos Musil, Andrej Jezik, Jana Horackova, Simeon Borko, Petr Kabourek, Jirí Damborský, David Bednar

Briefings Bioinform., November, 2023

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

Ondrej Vavra, Jakub Beránek, Jan Stourac, Martin Surkovský, Jiri Filipovic, Jirí Damborský, Jan Martinovic, David Bednar

Bioinform., August, 2023

sMolBoxes: Dataflow Model for Molecular Dynamics Exploration.

Pavol Ulbrich, Manuela Waldner, Katarína Furmanová, Sérgio M. Marques, David Bednár, Barbora Kozlíková, Jan Byska

IEEE Trans. Vis. Comput. Graph., 2023

2022

PDBe-KB: collaboratively defining the biological context of structural data.

Mihaly Varadi, Stephen Anyango, David R. Armstrong, John M. Berrisford, Preeti Choudhary, Mandar S. Deshpande, Nurul Nadzirin, Sreenath Nair, Lukás Pravda, Ahsan Tanweer, Bissan Al-Lazikani, Claudia Andreini, Geoffrey J. Barton, David Bednar, Karel Berka, Tom L. Blundell, Kelly Brock, José María Carazo, Jirí Damborský, Alessia David, Sucharita Dey, Roland L. Dunbrack Jr., Juan Fernández-Recio, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas A. Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Nir London, José Ramón Macías, Mallur Srivatsan Madhusudhan, Debora S. Marks, Lennart Martens, Stuart A McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Pawel Rubach, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar Sánchez Sorzano, Jan Stourac, Joanna I. Sulkowska, Radka Svobodová Vareková, Natalia Tichshenko, Silvio C. E. Tosatto, Wim F. Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar

Nucleic Acids Res., 2022

LoopGrafter: a web tool for transplanting dynamical loops for protein engineering.

Joan Planas-Iglesias, Filip Opálený, Pavol Ulbrich, Jan Stourac, Zainab K. Sanusi, Gaspar R. P. Pinto, Andrea Schenkmayerova, Jan Byska, Jirí Damborský, Barbora Kozlíková, David Bednar

Nucleic Acids Res., 2022

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

Javier L. Baylon, Oleg Ursu, Anja Muzdalo, Anne Mai Wassermann, Gregory L. Adams, Martin Spale, Petr Mejzlík, Anna Gromek, Viktor Pisarenko, Dzianis Hancharyk, Esteban Jenkins, David Bednar, Charlie Chang, Kamila Clarova, Meir Glick, Danny A. Bitton

J. Chem. Inf. Model., 2022

2021

FireProtDB: database of manually curated protein stability data.

Jan Stourac, Juraj Dubrava, Milos Musil, Jana Horackova, Jirí Damborský, Stanislav Mazurenko, David Bednar

Nucleic Acids Res., 2021

SoluProt: prediction of soluble protein expression in Escherichia coli.

Jirí Hon, Martin Marusiak, Tomás Martínek, Antonin Kunka, Jaroslav Zendulka, David Bednar, Jirí Damborský

Bioinform., 2021

2020

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

Jiri Filipovic, Ondrej Vávra, Jan Plhak, David Bednar, Sérgio M. Marques, Jan Brezovsky, Ludek Matyska, Jirí Damborský

IEEE ACM Trans. Comput. Biol. Bioinform., 2020

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

Jirí Hon, Simeon Borko, Jan Stourac, Zbynek Prokop, Jaroslav Zendulka, David Bednar, Tomás Martínek, Jirí Damborský

Nucleic Acids Res., 2020

DockVis: Visual Analysis of Molecular Docking Trajectories.

Katarína Furmanová, Ondrej Vávra, Barbora Kozlíková, Jirí Damborský, Vojtech Vonásek, David Bednar, Jan Byska

Comput. Graph. Forum, 2020

2019

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

Jan Stourac, Ondrej Vavra, Piia Kokkonen, Jiri Filipovic, Gaspar R. P. Pinto, Jan Brezovsky, Jirí Damborský, David Bednar

Nucleic Acids Res., 2019

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

Ondrej Vavra, Jiri Filipovic, Jan Plhak, David Bednar, Sérgio M. Marques, Jan Brezovsky, Jan Stourac, Ludek Matyska, Jirí Damborský

Bioinform., 2019

2018

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

Lenka Sumbalova, Jan Stourac, Tomás Martínek, David Bednar, Jirí Damborský

Nucleic Acids Res., 2018

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

Stanislav Mazurenko, Jan Stourac, Antonin Kunka, Sava Nedeljkovic, David Bednar, Zbynek Prokop, Jirí Damborský

Nucleic Acids Res., 2018

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

Adam Jurcík, David Bednar, Jan Byska, Sérgio M. Marques, Katarína Furmanová, Lukas Daniel, Piia Kokkonen, Jan Brezovsky, Ondrej Strnad, Jan Stourac, Antonín Pavelka, Martin Manak, Jirí Damborský, Barbora Kozlíková

Bioinform., 2018

2017

FireProt: web server for automated design of thermostable proteins.

Milos Musil, Jan Stourac, Jaroslav Bendl, Jan Brezovsky, Zbynek Prokop, Jaroslav Zendulka, Tomás Martínek, David Bednar, Jirí Damborský

Nucleic Acids Res., 2017

2015

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

David Bednar, Koen Beerens, Eva Sebestova, Jaroslav Bendl, Sagar D. Khare, Radka Chaloupkova, Zbynek Prokop, Jan Brezovsky, David Baker, Jirí Damborský

PLoS Comput. Biol., 2015

2014

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

Barbora Kozlíková, Eva Sebestova, Vilém Sustr, Jan Brezovsky, Ondrej Strnad, Lukas Daniel, David Bednar, Antonín Pavelka, Martin Manak, Martin Bezdeka, Petr Benes, Matus Kotry, Artur Góra, Jirí Damborský, Jiri Sochor

Bioinform., 2014

2011

Index-based n-gram extraction from large document collections.

Michal Krátký, Radim Baca, David Bednar, Jirí Walder, Jiri Dvorský, Peter Chovanec

Proceedings of the Sixth IEEE International Conference on Digital Information Management, 2011

Flexible Cache for Database Management Systems.

Radim Baca, David Bednar

Proceedings of the Dateso 2011: Annual International Workshop on DAtabases, 2011