AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules
Ionescu, Crina-Maria, Sehnal, David, Falginella, Francesco L., Pant, Purbaj, Pravda, Lukáš, Bouchal, Tomáš, Svobodová Vařeková, Radka, Geidl, Stanislav, Koča, Jaroslav
Published in Journal of cheminformatics (22.10.2015)
Published in Journal of cheminformatics (22.10.2015)
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Predicting pKa Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes
SVOBODOVA VAREKOVA, Radka, GEIDL, Stanislav, IONESCU, Crina-Maria, SKREHOTA, Ondřej, KUDERA, Michal, SEHNAL, David, BOUCHAL, Tomas, ABAGYAN, Ruben, HUBER, Heinrich J, KOCA, Jaroslav
Published in Journal of chemical information and modeling (22.08.2011)
Published in Journal of chemical information and modeling (22.08.2011)
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SiteBinder – an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs
Sehnal, David, Vařeková, Radka Svobodová, Huber, Heinrich J, Geidl, Stanislav, Ionescu, Crina-Maria, Wimmerová, Michaela, Koča, Jaroslav
Published in Journal of cheminformatics (01.05.2012)
Published in Journal of cheminformatics (01.05.2012)
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QSPR designer – employ your own descriptors in the automated QSAR modeling process
Skřehota, Ondřej, Vařeková, Radka Svobodová, Geidl, Stanislav, Kudera, Michal, Sehnal, David, Ionescu, Crina-Maria, Žídek, Jan, Koča, Jaroslav
Published in Journal of cheminformatics (01.05.2012)
Published in Journal of cheminformatics (01.05.2012)
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How the methodology of 3D structure preparation influences the quality of QSPR models?
Geidl, Stanislav, Beránek, Roman, Vařeková, Radka Svobodová, Bouchal, Tomáš, Brumovský, Miroslav, Kudera, Michal, Skřehota, Ondřej, Koča, Jaroslav
Published in Journal of cheminformatics (01.05.2012)
Published in Journal of cheminformatics (01.05.2012)
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Journal Article
How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction?
Geidl, Stanislav, Svobodová Vařeková, Radka, Bendová, Veronika, Petrusek, Lukáš, Ionescu, Crina-Maria, Jurka, Zdeněk, Abagyan, Ruben, Koča, Jaroslav
Published in Journal of chemical information and modeling (22.06.2015)
Published in Journal of chemical information and modeling (22.06.2015)
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ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank
Sehnal, David, Svobodová Vařeková, Radka, Pravda, Lukáš, Ionescu, Crina-Maria, Geidl, Stanislav, Horský, Vladimír, Jaiswal, Deepti, Wimmerová, Michaela, Koča, Jaroslav
Published in Nucleic acids research (28.01.2015)
Published in Nucleic acids research (28.01.2015)
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Journal Article
How Does the Methodology of 3D Structure Preparation Influence the Quality of p K a Prediction?
Geidl, Stanislav, Svobodová Vařeková, Radka, Bendová, Veronika, Petrusek, Lukáš, Ionescu, Crina-Maria, Jurka, Zdeněk, Abagyan, Ruben, Koča, Jaroslav
Published in Journal of chemical information and modeling (22.06.2015)
Published in Journal of chemical information and modeling (22.06.2015)
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Journal Article
How Does the Methodology of 3D Structure Preparation Influence the Quality of pK^sub a^ Prediction?
Geidl, Stanislav, Vareková, Radka Svobodová, Bendová, Veronika, Petrusek, Luká, Ionescu, Crina-Maria, Jurka, Zdenek, Abagyan, Ruben, Koca, Jaroslav
Published in Journal of chemical information and modeling (22.06.2015)
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Published in Journal of chemical information and modeling (22.06.2015)
Journal Article
Predicting pK a Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes
Svobodová Vařeková, Radka, Geidl, Stanislav, Ionescu, Crina-Maria, Skřehota, Ondřej, Kudera, Michal, Sehnal, David, Bouchal, Tomáš, Abagyan, Ruben, Huber, Heinrich J, Koča, Jaroslav
Published in Journal of chemical information and modeling (22.08.2011)
Published in Journal of chemical information and modeling (22.08.2011)
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Journal Article
How Does the Methodology of 3D Structure Preparation Influence the Quality of pK a Prediction?
Geidl, Stanislav, Svobodová Vařeková, Radka, Bendová, Veronika, Petrusek, Lukáš, Ionescu, Crina-Maria, Jurka, Zdeněk, Abagyan, Ruben, Koča, Jaroslav
Published in Journal of chemical information and modeling (01.06.2015)
Published in Journal of chemical information and modeling (01.06.2015)
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High-quality and universal empirical atomic charges for chemoinformatics applications
Geidl, Stanislav, Bouchal, Tomáš, Raček, Tomáš, Svobodová Vařeková, Radka, Hejret, Václav, Křenek, Aleš, Abagyan, Ruben, Koča, Jaroslav
Published in Journal of cheminformatics (02.12.2015)
Published in Journal of cheminformatics (02.12.2015)
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Journal Article
MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes
Vařeková, Radka Svobodová, Jaiswal, Deepti, Sehnal, David, Ionescu, Crina-Maria, Geidl, Stanislav, Pravda, Lukáš, Horský, Vladimír, Wimmerová, Michaela, Koča, Jaroslav
Published in Nucleic acids research (01.07.2014)
Published in Nucleic acids research (01.07.2014)
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The Eighth Central European Conference "Chemistry towards Biology": Snapshot
Perczel, András, Atanasov, Atanas G, Sklenář, Vladimír, Nováček, Jiří, Papoušková, Veronika, Kadeřávek, Pavel, Žídek, Lukáš, Kozłowski, Henryk, Wątły, Joanna, Hecel, Aleksandra, Kołkowska, Paulina, Koča, Jaroslav, Svobodová-Vařeková, Radka, Pravda, Lukáš, Sehnal, David, Horský, Vladimír, Geidl, Stanislav, Enriz, Ricardo D, Matějka, Pavel, Jeništová, Adéla, Dendisová, Marcela, Kokaislová, Alžběta, Weissig, Volkmar, Olsen, Mark, Coffey, Aidan, Ajuebor, Jude, Keary, Ruth, Sanz-Gaitero, Marta, van Raaij, Mark J, McAuliffe, Olivia, Waltenberger, Birgit, Mocan, Andrei, Šmejkal, Karel, Heiss, Elke H, Diederich, Marc, Musioł, Robert, Košmrlj, Janez, Polański, Jarosław, Jampílek, Josef
Published in Molecules (Basel, Switzerland) (17.10.2016)
Published in Molecules (Basel, Switzerland) (17.10.2016)
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Journal Article
Conference Proceeding
NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges
Raček, Tomáš, Pazúriková, Jana, Svobodová Vařeková, Radka, Geidl, Stanislav, Křenek, Aleš, Falginella, Francesco Luca, Horský, Vladimír, Hejret, Václav, Koča, Jaroslav
Published in Journal of cheminformatics (17.10.2016)
Published in Journal of cheminformatics (17.10.2016)
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Journal Article
Predicting pK a values from EEM atomic charges
Vařeková, Radka Svobodová, Geidl, Stanislav, Ionescu, Crina-Maria, Skřehota, Ondřej, Bouchal, Tomáš, Sehnal, David, Abagyan, Ruben, Koča, Jaroslav
Published in Journal of cheminformatics (10.04.2013)
Published in Journal of cheminformatics (10.04.2013)
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Journal Article
SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs
Sehnal, David, Vařeková, Radka Svobodová, Huber, Heinrich J, Geidl, Stanislav, Ionescu, Crina-Maria, Wimmerová, Michaela, Koča, Jaroslav
Published in Journal of chemical information and modeling (27.02.2012)
Published in Journal of chemical information and modeling (27.02.2012)
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Journal Article
Predicting p K a Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes
Svobodová Vařeková, Radka, Geidl, Stanislav, Ionescu, Crina-Maria, Skřehota, Ondřej, Kudera, Michal, Sehnal, David, Bouchal, Tomáš, Abagyan, Ruben, Huber, Heinrich J., Koča, Jaroslav
Published in Journal of chemical information and modeling (22.08.2011)
Published in Journal of chemical information and modeling (22.08.2011)
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Journal Article
QM quality atomic charges for proteins
Geidl, Stanislav, Ionescu, Crina-Maria, Vařeková, Radka Svobodová, Koča, Jaroslav
Published in Journal of cheminformatics (11.03.2014)
Published in Journal of cheminformatics (11.03.2014)
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Journal Article