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ORCIDRadka Svobodová Vareková
Radka Svobodová Vařeková
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- unicode name: Radka Svobodová Vařeková
- affiliation: Masaryk University Brno, Czech Republic
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Journal Articles
- 2023
[j45]Ondrej Schindler
, Karel Berka, Alessio Cantara, Ales Krenek, Dominik Tichý, Tomás Racek, Radka Svobodová Vareková:
αCharges: partial atomic charges for AlphaFold structures in high quality. Nucleic Acids Res. 51(W1): 11-16 (2023)- [j44]Aliaksei Chareshneu, Adam Midlik, Crina-Maria Ionescu, Alexander S. Rose, Vladimír Horský, Alessio Cantara, Radka Svobodová Vareková, Karel Berka, David Sehnal:
Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations. Nucleic Acids Res. 51(W1): 326-330 (2023) - 2022
- [j43]Adam Midlik, Ivana Hutarová Vareková, Jan Hutar, Aliaksei Chareshneu, Karel Berka, Radka Svobodová Vareková:
OverProt: secondary structure consensus for protein families. Bioinform. 38(14): 3648-3650 (2022) - [j42]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) - 2021
- [j41]Ivana Hutarová Vareková, Jan Hutar, Adam Midlik, Vladimír Horský, Eva Hladká, Radka Svobodová Vareková, Karel Berka:
2DProts: database of family-wide protein secondary structure diagrams. Bioinform. 37(23): 4599-4601 (2021) - [j40]Ondrej Schindler, Tomás Racek, Aleksandra Marsavelski, Jaroslav Koca, Karel Berka, Radka Svobodová Vareková:
Optimized SQE atomic charges for peptides accessible via a web application. J. Cheminformatics 13(1): 45 (2021) - [j39]Ondrej Schindler, Tomás Racek, Aleksandra Marsavelski, Jaroslav Koca, Karel Berka, Radka Svobodová Vareková:
Correction to: Optimized SQE atomic charges for peptides accessible via a web application. J. Cheminformatics 13(1): 52 (2021) - [j38]Ian Sillitoe, Nicola Bordin, Natalie L. Dawson, Vaishali P. Waman, Paul Ashford, Harry M. Scholes, Camilla S. M. Pang, Laurel Woodridge, Clemens Rauer, Neeladri Sen, Mahnaz Abbasian, Sean Le Cornu, Su Datt Lam, Karel Berka, Ivana Hutarová Vareková, Radka Svobodová Vareková, Jonathan G. Lees, Christine A. Orengo:
CATH: increased structural coverage of functional space. Nucleic Acids Res. 49(Database-Issue): D266-D273 (2021) - [j37]David Sehnal, Sebastian Bittrich, Mandar S. Deshpande, Radka Svobodová Vareková, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K. Burley, Jaroslav Koca, Alexander S. Rose:
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res. 49(Webserver-Issue): 431-437 (2021) - 2020
- [j36]David R. Armstrong, John M. Berrisford, Matthew J. Conroy, Aleksandras Gutmanas, Stephen Anyango, Preeti Choudhary, Alice R. Clark, Jose M. Dana, Mandar S. Deshpande, Roisin Dunlop, Paul J. Gane, Romana Gáborová, Deepti Gupta, Pauline Haslam, Jaroslav Koca, Lora Mak, Saqib Mir, Abhik Mukhopadhyay, Nurul Nadzirin, Sreenath Nair, Typhaine Paysan-Lafosse, Lukás Pravda, David Sehnal, Osman Salih, Oliver S. Smart, James Tolchard, Mihaly Varadi, Radka Svobodová Vareková, Hossam Zaki, Gerard J. Kleywegt, Sameer Velankar:
PDBe: improved findability of macromolecular structure data in the PDB. Nucleic Acids Res. 48(Database-Issue): D335-D343 (2020) - [j35]Mihaly Varadi, John M. Berrisford, Mandar S. Deshpande, Sreenath Nair, Aleksandras Gutmanas, David R. Armstrong, Lukás Pravda, Bissan Al-Lazikani, Stephen Anyango, Geoffrey J. Barton, Karel Berka, Tom L. Blundell, Neera Borkakoti, Jose M. Dana, Sayoni Das, Sucharita Dey, Patrizio Di Micco, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Liang-Chin Huang, Rishabh Jain, Harry Jubb, Christos C. Kannas, Natarajan Kannan, Jaroslav Koca, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Fábio Madeira, M. S. Madhusudhan, Henry J. Martell, Stuart A. MacGowan, Jake E. McGreig, Saqib Mir, Abhik Mukhopadhyay, Luca Parca, Typhaine Paysan-Lafosse, Leandro G. Radusky, António J. M. Ribeiro, Luis Serrano, Ian Sillitoe, Gulzar Singh, Petr Skoda, Radka Svobodová Vareková, Jonathan D. Tyzack, Alfonso Valencia, Eloy D. Villasclaras-Fernández, Wim F. Vranken, Mark N. Wass, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar:
PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 48(Database-Issue): D344-D353 (2020) - [j34]Tomás Racek, Ondrej Schindler, Dominik Tousek, Vladimír Horský, Karel Berka, Jaroslav Koca, Radka Svobodová Vareková:
Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. Nucleic Acids Res. 48(Webserver-Issue): W591-W596 (2020) - [j33]David Sehnal, Sebastian Bittrich, Sameer Velankar, Jaroslav Koca, Radka Svobodová Vareková, Stephen K. Burley, Alexander S. Rose:
BinaryCIF and CIFTools - Lightweight, efficient and extensible macromolecular data management. PLoS Comput. Biol. 16(10) (2020) - 2019
- [j32]Vladimír Horský, Veronika Bendová, Dominik Tousek, Jaroslav Koca, Radka Svobodová Vareková:
ValTrendsDB: bringing Protein Data Bank validation information closer to the user. Bioinform. 35(24): 5389-5390 (2019) - 2018
- [j31]Lukás Pravda, David Sehnal, Radka Svobodová Vareková, Veronika Navrátilová, Dominik Tousek, Karel Berka, Michal Otyepka, Jaroslav Koca:
ChannelsDB: database of biomacromolecular tunnels and pores. Nucleic Acids Res. 46(Database-Issue): D399-D405 (2018) - [j30]Lukás Pravda, David Sehnal, Dominik Tousek, Veronika Navrátilová, Václav Bazgier, Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, Michal Otyepka:
MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Res. 46(Webserver-Issue): W368-W373 (2018) - 2016
- [j29]Tomás Racek, Jana Pazúriková, Radka Svobodová Vareková, Stanislav Geidl, Ales Krenek, Francesco L. Falginella, Vladimír Horský, Václav Hejret, Jaroslav Koca:
NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. J. Cheminformatics 8(1): 57:1-57:14 (2016) - [j28]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) - 2015
- [j27]Crina-Maria Ionescu, David Sehnal, Francesco L. Falginella, Purbaj Pant, Lukás Pravda, Tomás Bouchal, Radka Svobodová Vareková, Stanislav Geidl, Jaroslav Koca:
AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. J. Cheminformatics 7: 50:1-50:13 (2015) - [j26]Stanislav Geidl, Tomás Bouchal, Tomás Racek, Radka Svobodová Vareková, Václav Hejret, Ales Krenek, Ruben Abagyan, Jaroslav Koca:
High-quality and universal empirical atomic charges for chemoinformatics applications. J. Cheminformatics 7: 59:1-59:10 (2015) - [j25]Stanislav Geidl, Radka Svobodová Vareková, Veronika Bendová, Lukás Petrusek, Crina-Maria Ionescu, Zdenek Jurka, Ruben Abagyan, Jaroslav Koca:
How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction? J. Chem. Inf. Model. 55(6): 1088-1097 (2015) - [j24]David Sehnal, Radka Svobodová Vareková, Lukás Pravda, Crina-Maria Ionescu, Stanislav Geidl, Vladimír Horský, Deepti Jaiswal Kundu, Michaela Wimmerová, Jaroslav Koca:
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. Nucleic Acids Res. 43(Database-Issue): 369-375 (2015) - [j23]David Sehnal, Lukás Pravda, Radka Svobodová Vareková, Crina-Maria Ionescu, Jaroslav Koca:
PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. Nucleic Acids Res. 43(Webserver-Issue): W383-W388 (2015) - 2014
- [j22]Lukás Pravda, Karel Berka, Radka Svobodová Vareková, David Sehnal, Pavel Banás, Roman A. Laskowski, Jaroslav Koca, Michal Otyepka:
Anatomy of enzyme channels. BMC Bioinform. 15: 379 (2014) - [j21]Deepti Jaiswal Kundu, David Sehnal, Radka Svobodová Vareková, Crina-Maria Ionescu, Jaroslav Koca:
Consistency of sugar structures and their annotation in the PDB. J. Cheminformatics 6(S-1): 41 (2014) - [j20]Tomás Bouchal, Radka Svobodová Vareková, Tomás Racek, Crina-Maria Ionescu, Stanislav Geidl, Ales Krenek, Jaroslav Koca:
Empirical charges for chemoinformatics applications. J. Cheminformatics 6(S-1): 60 (2014) - [j19]Stanislav Geidl, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca:
QM quality atomic charges for proteins. J. Cheminformatics 6(S-1): 61 (2014) - [j18]Radka Svobodová Vareková, Deepti Jaiswal Kundu, David Sehnal, Crina-Maria Ionescu, Stanislav Geidl, Lukás Pravda, Vladimír Horský, Michaela Wimmerová, Jaroslav Koca:
MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. Nucleic Acids Res. 42(Webserver-Issue): 227-233 (2014) - 2013
- [j17]Radka Svobodová Vareková, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Tomás Bouchal, David Sehnal, Ruben Abagyan, Jaroslav Koca:
Predicting pKa values from EEM atomic charges. J. Cheminformatics 5: 18 (2013) - [j16]David Sehnal, Radka Svobodová Vareková, Karel Berka, Lukás Pravda, Veronika Navrátilová, Pavel Banás, Crina-Maria Ionescu, Michal Otyepka, Jaroslav Koca:
MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J. Cheminformatics 5: 39 (2013) - [j15]Crina-Maria Ionescu, Stanislav Geidl, Radka Svobodová Vareková, Jaroslav Koca:
Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. J. Chem. Inf. Model. 53(10): 2548-2558 (2013) - 2012
- [j14]Ondrej Skrehota, Radka Svobodová Vareková, Stanislav Geidl, Michal Kudera, David Sehnal, Crina-Maria Ionescu, Jan Zidek, Jaroslav Koca:
QSPR designer - employ your own descriptors in the automated QSAR modeling process. J. Cheminformatics 4(S-1): 37 (2012) - [j13]David Sehnal, Radka Svobodová Vareková, Heinrich J. Huber, Stanislav Geidl, Crina-Maria Ionescu, Michaela Wimmerová, Jaroslav Koca:
SiteBinder - an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs. J. Cheminformatics 4(S-1): 59 (2012) - [j12]Deepti Jaiswal Kundu, Radka Svobodová Vareková, Crina-Maria Ionescu, David Sehnal, Jaroslav Koca:
Searching for tunnels of proteins - comparison of approaches and available software tools. J. Cheminformatics 4(S-1): 60 (2012) - [j11]Stanislav Geidl, Roman Beránek, Radka Svobodová Vareková, Tomás Bouchal, Miroslav Brumovský, Michal Kudera, Ondrej Skrehota, Jaroslav Koca:
How the methodology of 3D structure preparation influences the quality of QSPR models? J. Cheminformatics 4(S-1): 61 (2012) - [j10]David Sehnal, Radka Svobodová Vareková, Heinrich J. Huber, Stanislav Geidl, Crina-Maria Ionescu, Michaela Wimmerová, Jaroslav Koca:
SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs. J. Chem. Inf. Model. 52(2): 343-359 (2012) - [j9]Karel Berka, Ondrej Hanák, David Sehnal, Pavel Banás, Veronika Navrátilová, Deepti Jaiswal Kundu, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca, Michal Otyepka:
MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res. 40(Web-Server-Issue): 222-227 (2012) - [j8]Crina-Maria Ionescu, Radka Svobodová Vareková, Jochen H. M. Prehn, Heinrich J. Huber, Jaroslav Koca:
Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation. PLoS Comput. Biol. 8(6) (2012) - 2011
- [j7]Ondrej Skrehota, Radka Svobodová Vareková, Stanislav Geidl, Michal Kudera, David Sehnal, Crina-Maria Ionescu, Jaroslav Koca:
QSPR designer - a program to design and evaluate QSPR models. Case study on pKa prediction. J. Cheminformatics 3(S-1): 16 (2011) - [j6]Radka Svobodová Vareková, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Michal Kudera, David Sehnal, Tomás Bouchal, Ruben Abagyan, Heinrich J. Huber, Jaroslav Koca:
Predicting pKa Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes. J. Chem. Inf. Model. 51(8): 1795-1806 (2011) - 2009
- [j5]Zuzana Jirousková, Radka Svobodová Vareková, Jakub Vanek, Jaroslav Koca:
Software news and updates electronegativity equalization method: Parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme. J. Comput. Chem. 30(7): 1174-1178 (2009) - 2008
- [j4]Radka Svobodová Vareková, Ivan Bradác, Martin Plchút, Michal Skrdla, Michael Wacenovsky, Helmuth Mahr, Georg Mayer, Herbert Tanner, Hermann Brugger, Josef Withalm, Peter Lederer, Heinrich J. Huber, Gerhard Gierlinger, Ronald Graf, Hakim Tafer, Ivo L. Hofacker, Peter Schuster, Martin Polcík:
www.rnaworkbench.com: A new program for analyzing RNA interference. Comput. Methods Programs Biomed. 90(1): 89-94 (2008) - [j3]Fergal P. Casey, Norman E. Davey, Ivan Baran, Radka Svobodová Vareková, Denis C. Shields:
Web Server To Identify Similarity of Amino Acid Motifs to Compounds (SAAMCO). J. Chem. Inf. Model. 48(7): 1524-1529 (2008) - 2007
- [j2]Ivan Baran, Radka Svobodová Vareková, Laavanya Parthasarathi, Simon Suchomel, Fergal P. Casey, Denis C. Shields:
Identification of Potential Small Molecule Peptidomimetics Similar to Motifs in Proteins. J. Chem. Inf. Model. 47(2): 464-474 (2007) - 2006
- [j1]Radka Svobodová Vareková, Jaroslav Koca:
Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method. J. Comput. Chem. 27(3): 396-405 (2006)
Conference and Workshop Papers
- 2018
- [c1]Mateusz Kuzak, Jen Harrow, Rafael C. Jiménez, Paula Andrea Martínez, Fotis E. Psomopoulos, Radka Svobodová Vareková, Allegra Via:
Lesson Development for Open Source Software Best Practices Adoption. eScience 2018: 19-20
Informal and Other Publications
- 2023
- [i3]Tomás Svoboda, Tomás Racek, Josef Handl, Jozef Sabo, Adrián Rosinec, Lukasz Opiola, Wojciech Jesionek, Milan Esner, Markéta Pernisová, Natallia Madzia Valasevich, Ales Krenek, Radka Svobodová Vareková:
Onedata4Sci: Life science data management solution based on Onedata. CoRR abs/2311.16712 (2023) - 2017
- [i2]Rafael C. Jiménez, Mateusz Kuzak, Monther Alhamdoosh, Michelle Barker, Bérénice Batut, Mikael Borg, Salvador Capella-Gutiérrez, Neil P. Chue Hong, Martin Cook, Manuel Corpas, Madison Flannery, Leyla J. García, Josep Lluis Gelpí, Simon L. Gladman, Carole A. Goble, Montserrat González Ferreiro, Alejandra N. González-Beltrán, Philippa C. Griffin, Björn A. Grüning, Jonas Hagberg, Petr Holub, Rob W. W. Hooft, Jon C. Ison, Daniel S. Katz, Brane Leskosek, Federico López-Gómez, Luis J. Oliveira, David Mellor, Rowland Mosbergen, Nicola J. Mulder, Yasset Pérez-Riverol, Robert Pergl, Horst Pichler, Bernard J. Pope, Ferran Sanz, Maria Victoria Schneider, Victoria Stodden, Radoslaw Suchecki, Radka Svobodová Vareková, Harry-Anton Talvik, Ilian T. Todorov, Andrew E. Treloar, Sonika Tyagi, Maarten van Gompel, Daniel Vaughan, Allegra Via, Xiaochuan Wang, Nathan S. Watson-Haigh, Steve Crouch:
Four simple recommendations to encourage best practices in research software. F1000Research 6: 876- (2017) - 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
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