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)

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)

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)

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)

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)

Finding enzyme cofactors in Protein Data Bank. - Abhik Mukhopadhyay; Neera Borkakoti; Lukás Pravda; Jonathan D. Tyzack; Janet M. Thornton; Sameer Velankar (Bioinform., 2019)

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)

PDBe-KB: a community-driven resource for structural and functional annotations. - Mihaly Varadi; John M. Berrisford; Mandar S. Deshpande; Sreenath Nair; Aleksandras Gutmanas; David R. Armstrong; Lukás Pravda; Bissan Al-Lazikani; Stephen Anyango; Geoffrey J. Barton; Karel Berka; Tom L. Blundell; et al. (Nucleic Acids Res., 2020)

PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data. - Sreenath Nair; Mihaly Varadi; Nurul Nadzirin; Lukás Pravda; Stephen Anyango; Saqib Mir; John M. Berrisford; David R. Armstrong; Aleksandras Gutmanas; Sameer Velankar (Bioinform., 2021)

PDBeCIF: an open-source mmCIF/CIF parsing and processing package. - Glen van Ginkel; Lukás Pravda; Jose M. Dana; Mihaly Varadi; Peter A. Keller; Stephen Anyango; Sameer Velankar (BMC Bioinform., 2021)

PDBe-KB: collaboratively defining the biological context of structural data. - Mihaly Varadi; Stephen Anyango; David R. Armstrong; John M. Berrisford; Preeti Choudhary; Mandar S. Deshpande; Nurul Nadzirin; Sreenath Nair; Lukás Pravda; Ahsan Tanweer; Bissan Al-Lazikani; Claudia Andreini; et al. (Nucleic Acids Res., 2022)

PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank. - Ibrahim Roshan Kunnakkattu; Preeti Choudhary; Lukás Pravda; Nurul Nadzirin; Oliver S. Smart; Qi Yuan; Stephen Anyango; Sreenath Nair; Mihaly Varadi; Sameer Velankar (J. Cheminformatics, 2023)

Improving generalisability of 3D binding affinity models in low data regimes. - Julia Buhmann; Ward Haddadin; Lukás Pravda; Alan Bilsland; Hagen Triendl (CoRR, 2024)