Jan Stourac

22 papers Journal 22
YearRankTypeTitle / Venue / Authors
2025 J jnl
Visual Support for the Loop Grafting Workflow on Proteins.
IEEE Trans. Vis. Comput. Graph.
Filip Opálený, Pavol Ulbrich, Joan Planas-Iglesias, Jan Byska, Jan Stourac, David Bednár, Katarína Furmanová, Barbora Kozlíková
2024 J jnl
A computational workflow for analysis of missense mutations in precision oncology.
J. Cheminformatics
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
2024 J jnl
Large-scale annotation of biochemically relevant pockets and tunnels in cognate enzyme-ligand complexes.
J. Cheminformatics
Ondrej Vavra, Jonathan D. Tyzack, Farzan Haddadi, Jan Stourac, Jirí Damborský, Stanislav Mazurenko, Janet M. Thornton, David Bednar
2024 J jnl
PredictONCO: a web tool supporting decision-making in precision oncology by extending the bioinformatics predictions with advanced computing and machine learning.
Briefings Bioinform.
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
2024 J jnl
Visual Support for the Loop Grafting Workflow on Proteins.
CoRR
Filip Opálený, Pavol Ulbrich, Joan Planas-Iglesias, Jan Byska, Jan Stourac, David Bednár, Katarína Furmanová, Barbora Kozlíková
2023 J jnl
pyCaverDock: Python implementation of the popular tool for analysis of ligand transport with advanced caching and batch calculation support.
Bioinform.
Ondrej Vavra, Jakub Beránek, Jan Stourac, Martin Surkovský, Jiri Filipovic, Jirí Damborský, Jan Martinovic, David Bednar
2022 J jnl
CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability.
Nucleic Acids Res.
Antonin Kunka, David Lacko, Jan Stourac, Jirí Damborský, Zbynek Prokop, Stanislav Mazurenko
2022 J jnl
LoopGrafter: a web tool for transplanting dynamical loops for protein engineering.
Nucleic Acids Res.
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
2022 J jnl
PDBe-KB: collaboratively defining the biological context of structural data.
Nucleic Acids Res.
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
2021 J jnl
FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction.
Briefings Bioinform.
Milos Musil, Rayyan T. Khan, Andy Beier, Jan Stourac, Hannes Konegger, Jirí Damborský, David Bednar
2021 J jnl
FireProtDB: database of manually curated protein stability data.
Nucleic Acids Res.
Jan Stourac, Juraj Dubrava, Milos Musil, Jana Horackova, Jirí Damborský, Stanislav Mazurenko, David Bednar
2020 J jnl
EnzymeMiner: automated mining of soluble enzymes with diverse structures, catalytic properties and stabilities.
Nucleic Acids Res.
Jirí Hon, Simeon Borko, Jan Stourac, Zbynek Prokop, Jaroslav Zendulka, David Bednar, Tomás Martínek, Jirí Damborský
2019 J jnl
Caver Web 1.0: identification of tunnels and channels in proteins and analysis of ligand transport.
Nucleic Acids Res.
Jan Stourac, Ondrej Vavra, Piia Kokkonen, Jiri Filipovic, Gaspar R. P. Pinto, Jan Brezovsky, Jirí Damborský, David Bednar
2019 J jnl
CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels.
Bioinform.
Ondrej Vavra, Jiri Filipovic, Jan Plhak, David Bednar, Sérgio M. Marques, Jan Brezovsky, Jan Stourac, Ludek Matyska, Jirí Damborský
2018 J jnl
CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories.
Bioinform.
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
2018 J jnl
CalFitter: a web server for analysis of protein thermal denaturation data.
Nucleic Acids Res.
Stanislav Mazurenko, Jan Stourac, Antonin Kunka, Sava Nedeljkovic, David Bednar, Zbynek Prokop, Jirí Damborský
2018 J jnl
HotSpot Wizard 3.0: web server for automated design of mutations and smart libraries based on sequence input information.
Nucleic Acids Res.
Lenka Sumbalova, Jan Stourac, Tomás Martínek, David Bednar, Jirí Damborský
2017 J jnl
FireProt: web server for automated design of thermostable proteins.
Nucleic Acids Res.
Milos Musil, Jan Stourac, Jaroslav Bendl, Jan Brezovsky, Zbynek Prokop, Jaroslav Zendulka, Tomás Martínek, David Bednar, Jirí Damborský
2016 J jnl
HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering.
Nucleic Acids Res.
Jaroslav Bendl, Jan Stourac, Eva Sebestova, Ondrej Vavra, Milos Musil, Jan Brezovsky, Jirí Damborský
2016 J jnl
PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.
PLoS Comput. Biol.
Jaroslav Bendl, Milos Musil, Jan Stourac, Jaroslav Zendulka, Jirí Damborský, Jan Brezovsky
2016 J jnl
Top 10 metrics for life science software good practices.
F1000Research
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
2014 J jnl
PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations.
PLoS Comput. Biol.
Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonín Pavelka, Eric D. Wieben, Jaroslav Zendulka, Jan Brezovsky, Jirí Damborský