QSPR designer - a program to design and evaluate QSPR models. Case study on pKa prediction. - Ondrej Skrehota; Radka Svobodová Vareková; Stanislav Geidl; Michal Kudera; David Sehnal; Crina-Maria Ionescu; Jaroslav Koca (J. Cheminformatics, 2011)

Predicting pKa Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes. - Radka Svobodová Vareková; Stanislav Geidl; Crina-Maria Ionescu; Ondrej Skrehota; Michal Kudera; David Sehnal; Tomás Bouchal; Ruben Abagyan; Heinrich J. Huber; Jaroslav Koca (J. Chem. Inf. Model., 2011)

Searching for tunnels of proteins - comparison of approaches and available software tools. - Deepti Jaiswal Kundu; Radka Svobodová Vareková; Crina-Maria Ionescu; David Sehnal; Jaroslav Koca (J. Cheminformatics, 2012)

SiteBinder - an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs. - David Sehnal; Radka Svobodová Vareková; Heinrich J. Huber; Stanislav Geidl; Crina-Maria Ionescu; Michaela Wimmerová; Jaroslav Koca (J. Cheminformatics, 2012)

QSPR designer - employ your own descriptors in the automated QSAR modeling process. - Ondrej Skrehota; Radka Svobodová Vareková; Stanislav Geidl; Michal Kudera; David Sehnal; Crina-Maria Ionescu; Jan Zidek; Jaroslav Koca (J. Cheminformatics, 2012)

SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs. - David Sehnal; Radka Svobodová Vareková; Heinrich J. Huber; Stanislav Geidl; Crina-Maria Ionescu; Michaela Wimmerová; Jaroslav Koca (J. Chem. Inf. Model., 2012)

MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels. - Karel Berka; Ondrej Hanák; David Sehnal; Pavel Banás; Veronika Navrátilová; Deepti Jaiswal Kundu; Crina-Maria Ionescu; Radka Svobodová Vareková; Jaroslav Koca; Michal Otyepka (Nucleic Acids Res., 2012)

Charge Profile Analysis Reveals That Activation of Pro-apoptotic Regulators Bax and Bak Relies on Charge Transfer Mediated Allosteric Regulation. - Crina-Maria Ionescu; Radka Svobodová Vareková; Jochen H. M. Prehn; Heinrich J. Huber; Jaroslav Koca (PLoS Comput. Biol., 2012)

MOLE 2.0: advanced approach for analysis of biomacromolecular channels. - David Sehnal; Radka Svobodová Vareková; Karel Berka; Lukás Pravda; Veronika Navrátilová; Pavel Banás; Crina-Maria Ionescu; Michal Otyepka; Jaroslav Koca (J. Cheminformatics, 2013)

Predicting pKa values from EEM atomic charges. - Radka Svobodová Vareková; Stanislav Geidl; Crina-Maria Ionescu; Ondrej Skrehota; Tomás Bouchal; David Sehnal; Ruben Abagyan; Jaroslav Koca (J. Cheminformatics, 2013)

Rapid Calculation of Accurate Atomic Charges for Proteins via the Electronegativity Equalization Method. - Crina-Maria Ionescu; Stanislav Geidl; Radka Svobodová Vareková; Jaroslav Koca (J. Chem. Inf. Model., 2013)

Empirical charges for chemoinformatics applications. - Tomás Bouchal; Radka Svobodová Vareková; Tomás Racek; Crina-Maria Ionescu; Stanislav Geidl; Ales Krenek; Jaroslav Koca (J. Cheminformatics, 2014)

QM quality atomic charges for proteins. - Stanislav Geidl; Crina-Maria Ionescu; Radka Svobodová Vareková; Jaroslav Koca (J. Cheminformatics, 2014)

Consistency of sugar structures and their annotation in the PDB. - Deepti Jaiswal Kundu; David Sehnal; Radka Svobodová Vareková; Crina-Maria Ionescu; Jaroslav Koca (J. Cheminformatics, 2014)

MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. - Radka Svobodová Vareková; Deepti Jaiswal Kundu; David Sehnal; Crina-Maria Ionescu; Stanislav Geidl; Lukás Pravda; Vladimír Horský; Michaela Wimmerová; Jaroslav Koca (Nucleic Acids Res., 2014)

AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. - Crina-Maria Ionescu; David Sehnal; Francesco L. Falginella; Purbaj Pant; Lukás Pravda; Tomás Bouchal; Radka Svobodová Vareková; Stanislav Geidl; Jaroslav Koca (J. Cheminformatics, 2015)

How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction? - Stanislav Geidl; Radka Svobodová Vareková; Veronika Bendová; Lukás Petrusek; Crina-Maria Ionescu; Zdenek Jurka; Ruben Abagyan; Jaroslav Koca (J. Chem. Inf. Model., 2015)

PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. - David Sehnal; Lukás Pravda; Radka Svobodová Vareková; Crina-Maria Ionescu; Jaroslav Koca (Nucleic Acids Res., 2015)

ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. - David Sehnal; Radka Svobodová Vareková; Lukás Pravda; Crina-Maria Ionescu; Stanislav Geidl; Vladimír Horský; Deepti Jaiswal Kundu; Michaela Wimmerová; Jaroslav Koca (Nucleic Acids Res., 2015)

CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing. - Ravi José Tristão Ramos; Allan Cézar de Azevedo Martins; Gabrielle da Silva Delgado; Crina-Maria Ionescu; Turán Peter Ürményi; Rosane Silva; Jaroslav Koca (Bioinform., 2017)

Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations. - Aliaksei Chareshneu; Adam Midlik; Crina-Maria Ionescu; Alexander S. Rose; Vladimír Horský; Alessio Cantara; Radka Svobodová Vareková; Karel Berka; David Sehnal (Nucleic Acids Res., 2023)