Radka Svobodová Vařeková
Radka Svobodová Vařeková
Verified email at chemi.muni.cz
TitleCited byYear
MOLE 2.0: advanced approach for analysis of biomacromolecular channels
D Sehnal, RS Vařeková, K Berka, L Pravda, V Navrátilová, P Banáš, ...
Journal of cheminformatics 5 (1), 39, 2013
1522013
PDBsum: Structural summaries of PDB entries
RA Laskowski, J Jabłońska, L Pravda, RS Vařeková, JM Thornton
Protein science 27 (1), 129-134, 2018
922018
MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels
K Berka, O Hanák, D Sehnal, P Banáš, V Navratilova, D Jaiswal, ...
Nucleic acids research 40 (W1), W222-W227, 2012
842012
Tools and data services registry: a community effort to document bioinformatics resources
J Ison, K Rapacki, H Ménager, M Kalaš, E Rydza, P Chmura, C Anthon, ...
Nucleic acids research 44 (D1), D38-D47, 2016
792016
LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data
D Sehnal, M Deshpande, RS Vařeková, S Mir, K Berka, A Midlik, L Pravda, ...
Nature methods 14 (12), 1121-1122, 2017
562017
Predicting pKa Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes
R Svobodová Vařeková, S Geidl, CM Ionescu, O Skrehota, M Kudera, ...
Journal of chemical information and modeling 51 (8), 1795-1806, 2011
472011
Anatomy of enzyme channels
L Pravda, K Berka, RS Vařeková, D Sehnal, P Banáš, RA Laskowski, ...
BMC bioinformatics 15 (1), 379, 2014
452014
Protein Data Bank: the single global archive for 3D macromolecular structure data
Nucleic acids research 47 (D1), D520-D528, 2019
442019
Outcome of the first wwPDB/CCDC/D3R ligand validation workshop
PD Adams, K Aertgeerts, C Bauer, JA Bell, HM Berman, TN Bhat, ...
Structure 24 (4), 502-508, 2016
402016
Four simple recommendations to encourage best practices in research software
RC Jiménez, M Kuzak, M Alhamdoosh, M Barker, B Batut, M Borg, ...
F1000Research 6, 2017
352017
MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update)
L Pravda, D Sehnal, D Toušek, V Navrátilová, V Bazgier, K Berka, ...
Nucleic acids research 46 (W1), W368-W373, 2018
242018
Electronegativity equalization method: parameterization and validation for large sets of organic, organohalogene and organometal molecule
RS Varekova, Z Jirouskova, J Vanek, S Suchomel, J Koca
International journal of molecular sciences 8 (7), 572-582, 2007
242007
AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules
CM Ionescu, D Sehnal, FL Falginella, P Pant, L Pravda, T Bouchal, ...
Journal of cheminformatics 7 (1), 50, 2015
232015
Electronegativity equalization method: parameterization and validation for organic molecules using the Merz-Kollman-Singh charge distribution scheme.
Z Jirouskova, RS Varekova, J Vanek, J Koca
Journal of computational chemistry 30 (7), 1174-1178, 2009
222009
Validation of ligands in macromolecular structures determined by X-ray crystallography
OS Smart, V Horský, S Gore, R Svobodová Vařeková, V Bendová, ...
Acta Crystallographica Section D: Structural Biology 74 (3), 228-236, 2018
192018
Identification of potential small molecule peptidomimetics similar to motifs in proteins
I Baran, RS Varekova, L Parthasarathi, S Suchomel, F Casey, DC Shields
Journal of chemical information and modeling 47 (2), 464-474, 2007
192007
Rapid calculation of accurate atomic charges for proteins via the electronegativity equalization method
CM Ionescu, S Geidl, R Svobodová Vařeková, J Koca
Journal of chemical information and modeling 53 (10), 2548-2558, 2013
172013
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank
D Sehnal, R Svobodová Vařeková, L Pravda, CM Ionescu, S Geidl, ...
Nucleic acids research 43 (D1), D369-D375, 2015
162015
Optimized and parallelized implementation of the electronegativity equalization method and the atom-bond electronegativity equalization method.
RS Vareková, J Koca
Journal of computational chemistry 27 (3), 396-405, 2006
152006
ChannelsDB: database of biomacromolecular tunnels and pores
L Pravda, D Sehnal, R Svobodová Vařeková, V Navrátilová, D Toušek, ...
Nucleic acids research 46 (D1), D399-D405, 2018
142018
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