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ORCIDJirí Damborský
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- affiliation: Masaryk University, Brno, Czech Republic
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Journal Articles
- 2023
[j37]Milos Musil, Andrej Jezik, Jana Horackova, Simeon Borko, Petr Kabourek, Jirí Damborský
, David Bednar:
FireProt 2.0: web-based platform for the fully automated design of thermostable proteins. Briefings Bioinform. 25(1) (2023)- [j36]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) - [j35]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
- [j34]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) - [j33]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) - [j32]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
- [j31]Jirí Hon, Martin Marusiak, Tomás Martínek, Antonin Kunka, Jaroslav Zendulka, David Bednar, Jirí Damborský:
SoluProt: prediction of soluble protein expression in Escherichia coli. Bioinform. 37(1): 23-28 (2021) - [j30]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
- [j29]Katarína Furmanová, Ondrej Vávra, Barbora Kozlíková, Jirí Damborský, Vojtech Vonásek, David Bednar, Jan Byska:
DockVis: Visual Analysis of Molecular Docking Trajectories. Comput. Graph. Forum 39(6): 452-464 (2020) - [j28]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) - [j27]Jiri Filipovic, Ondrej Vávra, Jan Plhak, David Bednar, Sérgio M. Marques, Jan Brezovsky, Ludek Matyska, Jirí Damborský:
CaverDock: A Novel Method for the Fast Analysis of Ligand Transport. IEEE ACM Trans. Comput. Biol. Bioinform. 17(5): 1625-1638 (2020) - 2019
- [j26]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) - [j25]Jan Byska, Thomas Trautner, Sérgio M. Marques, Jirí Damborský, Barbora Kozlíková, Manuela Waldner:
Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization. Comput. Graph. Forum 38(3): 441-453 (2019) - [j24]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
- [j23]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) - [j22]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) - [j21]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) - [j20]Zdenek Pilát, Martin Kizovský, Jan Jezek, Stanislav Krátký, Jaroslav Sobota, Martin Siler, Ota Samek, Tomas Buryska, Pavel Vanácek, Jirí Damborský, Zbynek Prokop, Pavel Zemánek:
Detection of Chloroalkanes by Surface-Enhanced Raman Spectroscopy in Microfluidic Chips. Sensors 18(10): 3212 (2018) - 2017
- [j19]Sérgio M. Marques, Zuzana Dunajova, Zbynek Prokop, Radka Chaloupkova, Jan Brezovsky, Jirí Damborský:
Catalytic Cycle of Haloalkane Dehalogenases Toward Unnatural Substrates Explored by Computational Modeling. J. Chem. Inf. Model. 57(8): 1970-1989 (2017) - [j18]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
- [j17]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) - [j16]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) - [j15]Antonín Pavelka, Eva Sebestova, Barbora Kozlíková, Jan Brezovsky, Jirí Sochor, Jirí Damborský:
CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules. IEEE ACM Trans. Comput. Biol. Bioinform. 13(3): 505-517 (2016) - 2015
- [j14]Lukas Daniel, Tomas Buryska, Zbynek Prokop, Jirí Damborský, Jan Brezovsky:
Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases Using in Silico Screening. J. Chem. Inf. Model. 55(1): 54-62 (2015) - [j13]David Bednar, Koen Beerens, Eva Sebestova, Jaroslav Bendl, Sagar D. Khare, Radka Chaloupkova, Zbynek Prokop, Jan Brezovsky, David Baker, Jirí Damborský:
FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. PLoS Comput. Biol. 11(11) (2015) - 2014
- [j12]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:
CAVER Analyst 1.0: graphic tool for interactive visualization and analysis of tunnels and channels in protein structures. Bioinform. 30(18): 2684-2685 (2014) - [j11]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) - 2012
- [j10]Eva Chovancová, Antonín Pavelka, Petr Benes, Ondrej Strnad, Jan Brezovsky, Barbora Kozlíková, Artur Góra, Vilém Sustr, Martin Klvana, Petr Medek, Lada Biedermannová, Jiri Sochor, Jirí Damborský:
CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures. PLoS Comput. Biol. 8(10) (2012) - 2009
- [j9]Antonín Pavelka, Eva Chovancová, Jirí Damborský:
HotSpot Wizard: a web server for identification of hot spots in protein engineering. Nucleic Acids Res. 37(Web-Server-Issue): 376-383 (2009) - 2006
- [j8]Martin Petrek, Michal Otyepka, Pavel Banás, Pavlína Kosinová, Jaroslav Koca, Jirí Damborský:
CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinform. 7: 316 (2006) - [j7]Pavel Banás, Michal Otyepka, Petr Jerábek, Martin Petrek, Jirí Damborský:
Mechanism of enhanced conversion of 1, 2, 3-trichloropropane by mutant haloalkane dehalogenase revealed by molecular modeling. J. Comput. Aided Mol. Des. 20(6): 375-383 (2006) - 2004
- [j6]Petr Dobes, Jan Kmunícek, Vladimír Mikes, Jirí Damborský:
Binding of Fatty Acids to beta-Cryptogein: Quantitative Structure-Activity Relationships and Design of Selective Protein Mutants. J. Chem. Inf. Model. 44(6): 2126-2132 (2004) - 2003
- [j5]Jan Kmunícek, Michal Bohác, Santos Luengo, Federico Gago, Rebecca C. Wade, Jirí Damborský:
Comparative binding energy analysis of haloalkane dehalogenase substrates: Modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations. J. Comput. Aided Mol. Des. 17(5-6): 299-311 (2003) - 2000
- [j4]Martin Prokop, Jirí Damborský, Jaroslav Koca:
TRITON: in silico construction of protein mutants and prediction of their activities. Bioinform. 16(9): 845-846 (2000) - [j3]Michal Cajan, Jirí Damborský, Ivan Stibor, Jaroslav Koca:
Stability of Complexes of Aromatic Amides with Bromide Anion: Quantitative Structure-Property Relationships. J. Chem. Inf. Comput. Sci. 40(5): 1151-1157 (2000) - 1998
- [j2]Michal Kutý, Jirí Damborský, Martin Prokop, Jaroslav Koca:
A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase. 2. Quantum Chemical Study of Complete Reaction Mechanism. J. Chem. Inf. Comput. Sci. 38(4): 736-741 (1998) - 1997
- [j1]Jirí Damborský, Michal Kutý, Miroslav Nemec, Jaroslav Koca:
A Molecular Modeling Study of the Catalytic Mechanism of Haloalkane Dehalogenase: 1. Quantum Chemical Study of the First Reaction Step. J. Chem. Inf. Comput. Sci. 37(3): 562-568 (1997)
Conference and Workshop Papers
- 2017
- [c3]Stanislav Mazurenko, Jirí Damborský, Zbynek Prokop:
Multi-Enzyme Pathway Optimisation Through Star-Shaped Reachable Sets. PACBB 2017: 9-17 - [c2]Viktor Vad, Jan Byska, Adam Jurcík, Ivan Viola, M. Eduard Gröller, Helwig Hauser, Sérgio M. Marques, Jirí Damborský, Barbora Kozlíková:
Watergate: Visual Exploration of Water Trajectories in Protein Dynamics. VCBM 2017: 33-42 - 2011
- [c1]Jana Klánová, Ludek Bláha, Jirí Damborský, Petr Klán, Ladislav Dusek, Ivan Holoubek:
CETOCOEN Project: From the Laboratory to the Field and Beyond. ISESS 2011: 491-499
Informal and Other Publications
- 2023
- [i1]Anton Bushuiev, Roman Bushuiev, Anatolii Filkin, Petr Kouba, Marketa Gabrielova, Michal Gabriel, Jirí Sedlár, Tomás Pluskal, Jirí Damborský, Stanislav Mazurenko, Josef Sivic:
Learning to design protein-protein interactions with enhanced generalization. CoRR abs/2310.18515 (2023)
Coauthor Index
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