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)

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)

Anatomy of enzyme channels. - Lukás Pravda; Karel Berka; Radka Svobodová Vareková; David Sehnal; Pavel Banás; Roman A. Laskowski; Jaroslav Koca; Michal Otyepka (BMC Bioinform., 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)

Method of Solving the Volume Between Triangulated Mesh Surfaces. - Szymon Tengler; David Sehnal (ISAT (3), 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)

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)

Mol*: Towards a Common Library and Tools for Web Molecular Graphics. - David Sehnal; Alexander S. Rose; Jaroslav Koca; Stephen K. Burley; Sameer Velankar (MolVa@EuroVis, 2018)

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. - Saqib Mir; Younes Alhroub; Stephen Anyango; David R. Armstrong; John M. Berrisford; Alice R. Clark; Matthew J. Conroy; Jose M. Dana; Mandar S. Deshpande; Deepti Gupta; Aleksandras Gutmanas; Pauline Haslam; et al. (Nucleic Acids Res., 2018)

MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). - Lukás Pravda; David Sehnal; Dominik Tousek; Veronika Navrátilová; Václav Bazgier; Karel Berka; Radka Svobodová Vareková; Jaroslav Koca; Michal Otyepka (Nucleic Acids Res., 2018)

ChannelsDB: database of biomacromolecular tunnels and pores. - Lukás Pravda; David Sehnal; Radka Svobodová Vareková; Veronika Navrátilová; Dominik Tousek; Karel Berka; Michal Otyepka; Jaroslav Koca (Nucleic Acids Res., 2018)

PDBe: improved findability of macromolecular structure data in the PDB. - 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; et al. (Nucleic Acids Res., 2020)

BinaryCIF and CIFTools - Lightweight, efficient and extensible macromolecular data management. - David Sehnal; Sebastian Bittrich; Sameer Velankar; Jaroslav Koca; Radka Svobodová Vareková; Stephen K. Burley; Alexander S. Rose (PLoS Comput. Biol., 2020)

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. - David Sehnal; Sebastian Bittrich; Mandar S. Deshpande; Radka Svobodová Vareková; Karel Berka; Václav Bazgier; Sameer Velankar; Stephen K. Burley; Jaroslav Koca; Alexander S. Rose (Nucleic Acids Res., 2021)

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)

PDBImages: a command-line tool for automated macromolecular structure visualization. - Adam Midlik; Sreenath Nair; Stephen Anyango; Mandar S. Deshpande; David Sehnal; Mihaly Varadi; Sameer Velankar (Bioinform., 2023)