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Journal Articles
- 2024
[j18]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:
A computational workflow for analysis of missense mutations in precision oncology. J. Cheminformatics 16(1): 86 (2024)- [j17]Ondrej Vavra, Jonathan D. Tyzack, Farzan Haddadi, Jan Stourac, Jirí Damborský, Stanislav Mazurenko, Janet M. Thornton, David Bednar:
Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes. J. Cheminformatics 16(1): 114 (2024) - 2023
- [j16]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:
PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning. Briefings Bioinform. 25(1) (2023) - [j15]Ondrej Vavra, Jakub Beránek, Jan Stourac, Martin Surkovský, Jiri Filipovic, Jirí Damborský, Jan Martinovic, David Bednar:
pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support. Bioinform. 39(8) (2023) - 2022
- [j14]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:
PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Res. 50(D1): 534-542 (2022) - [j13]Antonin Kunka, David Lacko, Jan Stourac, Jirí Damborský, Zbynek Prokop, Stanislav Mazurenko:
CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability. Nucleic Acids Res. 50(W1): 145-151 (2022) - [j12]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:
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. Nucleic Acids Res. 50(W1): 465-473 (2022) - 2021
- [j11]Jan Stourac, Juraj Dubrava, Milos Musil, Jana Horackova, Jirí Damborský, Stanislav Mazurenko, David Bednar:
FireProtDB: database of manually curated protein stability data. Nucleic Acids Res. 49(Database-Issue): D319-D324 (2021) - 2020
- [j10]Jirí Hon, Simeon Borko, Jan Stourac, Zbynek Prokop, Jaroslav Zendulka, David Bednar, Tomás Martínek, Jirí Damborský:
EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities. Nucleic Acids Res. 48(Webserver-Issue): W104-W109 (2020) - 2019
- [j9]Ondrej Vavra, Jiri Filipovic, Jan Plhak, David Bednar, Sérgio M. Marques, Jan Brezovsky, Jan Stourac, Ludek Matyska, Jirí Damborský:
CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinform. 35(23): 4986-4993 (2019) - [j8]Jan Stourac, Ondrej Vavra, Piia Kokkonen, Jiri Filipovic, Gaspar R. P. Pinto, Jan Brezovsky, Jirí Damborský, David Bednar:
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport. Nucleic Acids Res. 47(Webserver-Issue): W414-W422 (2019) - 2018
- [j7]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:
CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories. Bioinform. 34(20): 3586-3588 (2018) - [j6]Stanislav Mazurenko, Jan Stourac, Antonin Kunka, Sava Nedeljkovic, David Bednar, Zbynek Prokop, Jirí Damborský:
CalFitter: a web server for analysis of protein thermal denaturation data. Nucleic Acids Res. 46(Webserver-Issue): W344-W349 (2018) - [j5]Lenka Sumbalova, Jan Stourac, Tomás Martínek, David Bednar, Jirí Damborský:
HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information. Nucleic Acids Res. 46(Webserver-Issue): W356-W362 (2018) - 2017
- [j4]Milos Musil, Jan Stourac, Jaroslav Bendl, Jan Brezovsky, Zbynek Prokop, Jaroslav Zendulka, Tomás Martínek, David Bednar, Jirí Damborský:
FireProt: web server for automated design of thermostable proteins. Nucleic Acids Res. 45(Webserver-Issue): W393-W399 (2017) - 2016
- [j3]Jaroslav Bendl, Jan Stourac, Eva Sebestova, Ondrej Vavra, Milos Musil, Jan Brezovsky, Jirí Damborský:
HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering. Nucleic Acids Res. 44(Webserver-Issue): W479-W487 (2016) - [j2]Jaroslav Bendl, Milos Musil, Jan Stourac, Jaroslav Zendulka, Jirí Damborský, Jan Brezovsky:
PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions. PLoS Comput. Biol. 12(5) (2016) - 2014
- [j1]Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonín Pavelka, Eric D. Wieben, Jaroslav Zendulka, Jan Brezovsky, Jirí Damborský:
PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations. PLoS Comput. Biol. 10(1) (2014)
Informal and Other Publications
- 2024
- [i2]Filip Opálený, Pavol Ulbrich, Joan Planas-Iglesias, Jan Byska, Jan Stourac, David Bednár, Katarína Furmanová, Barbora Kozlíková:
Visual Support for the Loop Grafting Workflow on Proteins. CoRR abs/2407.20054 (2024) - 2016
- [i1]Haydee Artaza, Neil P. Chue Hong, Manuel Corpas, Angel Corpuz, Rob W. W. Hooft, Rafael C. Jiménez, Brane Leskosek, Brett G. Olivier, Jan Stourac, Radka Svobodová Vareková, Thomas Van Parys, Daniel Vaughan:
Top 10 metrics for life science software good practices. F1000Research 5: 2000 (2016)
Coauthor Index
aka: David Bednár
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