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2020 – today
- 2024
[j19]Carlos Eduardo Sequeiros-Borja
, Bartlomiej Surpeta, Aravind Selvaram Thirunavukarasu, Cedrix Jurgal Dongmo Foumthuim, Igor Marchlewski, Jan Brezovsky:
Water will Find Its Way: Transport through Narrow Tunnels in Hydrolases. J. Chem. Inf. Model. 64(15): 6014-6025 (2024)- [j18]Nishita Mandal, Bartlomiej Surpeta, Jan Brezovsky:
Reinforcing Tunnel Network Exploration in Proteins Using Gaussian Accelerated Molecular Dynamics. J. Chem. Inf. Model. 64(16): 6623-6635 (2024) - 2022
- [j17]Jan Brezovsky, Aravind Selvaram Thirunavukarasu, Bartlomiej Surpeta, Carlos Eduardo Sequeiros-Borja, Nishita Mandal, Dheeraj Kumar Sarkar, Cedrix Jurgal Dongmo Foumthuim, Nikhil Agrawal:
TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them. Bioinform. 38(6): 1752-1753 (2022) - 2021
- [j16]Carlos Eduardo Sequeiros-Borja, Bartlomiej Surpeta, Jan Brezovsky:
Recent advances in user-friendly computational tools to engineer protein function. Briefings Bioinform. 22(3) (2021) - 2020
- [j15]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)
2010 – 2019
- 2019
- [j14]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) - [j13]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
- [j12]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) - 2017
- [j11]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) - [j10]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
- [j9]Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jiménez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak:
Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 44(Database-Issue): 38-47 (2016) - [j8]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) - [j7]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) - [j6]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
- [j5]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) - [j4]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
- [j3]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) - [j2]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
- [j1]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)
Coauthor Index
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