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)

How the methodology of 3D structure preparation influences the quality of QSPR models? - Stanislav Geidl; Roman Beránek; Radka Svobodová Vareková; Tomás Bouchal; Miroslav Brumovský; Michal Kudera; Ondrej Skrehota; 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)

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)

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)

High-quality and universal empirical atomic charges for chemoinformatics applications. - Stanislav Geidl; Tomás Bouchal; Tomás Racek; Radka Svobodová Vareková; Václav Hejret; Ales Krenek; Ruben Abagyan; Jaroslav Koca (J. Cheminformatics, 2015)

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)

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)

NEEMP: software for validation, accurate calculation and fast parameterization of EEM charges. - Tomás Racek; Jana Pazúriková; Radka Svobodová Vareková; Stanislav Geidl; Ales Krenek; Francesco L. Falginella; Vladimír Horský; Václav Hejret; Jaroslav Koca (J. Cheminformatics, 2016)