Lukás Pravda

16 papers Journal 16
YearRankTypeTitle / Venue / Authors
2024 J jnl
Improving generalisability of 3D binding affinity models in low data regimes.
CoRR
Julia Buhmann, Ward Haddadin, Lukás Pravda, Alan Bilsland, Hagen Triendl
2023 J jnl
PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank.
J. Cheminformatics
Ibrahim Roshan Kunnakkattu, Preeti Choudhary, Lukás Pravda, Nurul Nadzirin, Oliver S. Smart, Qi Yuan, Stephen Anyango, Sreenath Nair, Mihaly Varadi, Sameer Velankar
2022 J jnl
PDBe-KB: collaboratively defining the biological context of structural data.
Nucleic Acids Res.
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, Geoffrey J. Barton, David Bednar, Karel Berka, Tom L. Blundell, Kelly Brock, José María Carazo, Jirí Damborský, Alessia David, Sucharita Dey, Roland L. Dunbrack Jr., Juan Fernández-Recio, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Thomas A. Hopf, David Jakubec, Natarajan Kannan, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Nir London, José Ramón Macías, Mallur Srivatsan Madhusudhan, Debora S. Marks, Lennart Martens, Stuart A McGowan, Jake E. McGreig, Vivek Modi, R. Gonzalo Parra, Gerardo Pepe, Damiano Piovesan, Jaime Prilusky, Valeria Putignano, Leandro G. Radusky, Pathmanaban Ramasamy, Atilio O. Rausch, Nathalie Reuter, Luis A. Rodriguez, Nathan J. Rollins, Antonio Rosato, Pawel Rubach, Luis Serrano, Gulzar Singh, Petr Skoda, Carlos Oscar Sánchez Sorzano, Jan Stourac, Joanna I. Sulkowska, Radka Svobodová Vareková, Natalia Tichshenko, Silvio C. E. Tosatto, Wim F. Vranken, Mark N. Wass, Dandan Xue, Daniel Zaidman, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar
2021 J jnl
PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data.
Bioinform.
Sreenath Nair, Mihaly Varadi, Nurul Nadzirin, Lukás Pravda, Stephen Anyango, Saqib Mir, John M. Berrisford, David R. Armstrong, Aleksandras Gutmanas, Sameer Velankar
2021 J jnl
PDBeCIF: an open-source mmCIF/CIF parsing and processing package.
BMC Bioinform.
Glen van Ginkel, Lukás Pravda, Jose M. Dana, Mihaly Varadi, Peter A. Keller, Stephen Anyango, Sameer Velankar
2020 J jnl
PDBe-KB: a community-driven resource for structural and functional annotations.
Nucleic Acids Res.
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, Neera Borkakoti, Jose M. Dana, Sayoni Das, Sucharita Dey, Patrizio Di Micco, Franca Fraternali, Toby J. Gibson, Manuela Helmer-Citterich, David Hoksza, Liang-Chin Huang, Rishabh Jain, Harry Jubb, Christos C. Kannas, Natarajan Kannan, Jaroslav Koca, Radoslav Krivák, Manjeet Kumar, Emmanuel D. Levy, Fábio Madeira, M. S. Madhusudhan, Henry J. Martell, Stuart A. MacGowan, Jake E. McGreig, Saqib Mir, Abhik Mukhopadhyay, Luca Parca, Typhaine Paysan-Lafosse, Leandro G. Radusky, António J. M. Ribeiro, Luis Serrano, Ian Sillitoe, Gulzar Singh, Petr Skoda, Radka Svobodová Vareková, Jonathan D. Tyzack, Alfonso Valencia, Eloy D. Villasclaras-Fernández, Wim F. Vranken, Mark N. Wass, Janet M. Thornton, Michael J. E. Sternberg, Christine A. Orengo, Sameer Velankar
2020 J jnl
PDBe: improved findability of macromolecular structure data in the PDB.
Nucleic Acids Res.
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, Deepti Gupta, Pauline Haslam, Jaroslav Koca, Lora Mak, Saqib Mir, Abhik Mukhopadhyay, Nurul Nadzirin, Sreenath Nair, Typhaine Paysan-Lafosse, Lukás Pravda, David Sehnal, Osman Salih, Oliver S. Smart, James Tolchard, Mihaly Varadi, Radka Svobodová Vareková, Hossam Zaki, Gerard J. Kleywegt, Sameer Velankar
2019 J jnl
Finding enzyme cofactors in Protein Data Bank.
Bioinform.
Abhik Mukhopadhyay, Neera Borkakoti, Lukás Pravda, Jonathan D. Tyzack, Janet M. Thornton, Sameer Velankar
2018 J jnl
ChannelsDB: database of biomacromolecular tunnels and pores.
Nucleic Acids Res.
Lukás Pravda, David Sehnal, Radka Svobodová Vareková, Veronika Navrátilová, Dominik Tousek, Karel Berka, Michal Otyepka, Jaroslav Koca
2018 J jnl
MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update).
Nucleic Acids Res.
Lukás Pravda, David Sehnal, Dominik Tousek, Veronika Navrátilová, Václav Bazgier, Karel Berka, Radka Svobodová Vareková, Jaroslav Koca, Michal Otyepka
2015 J jnl
AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules.
J. Cheminformatics
Crina-Maria Ionescu, David Sehnal, Francesco L. Falginella, Purbaj Pant, Lukás Pravda, Tomás Bouchal, Radka Svobodová Vareková, Stanislav Geidl, Jaroslav Koca
2015 J jnl
PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank.
Nucleic Acids Res.
David Sehnal, Lukás Pravda, Radka Svobodová Vareková, Crina-Maria Ionescu, Jaroslav Koca
2015 J jnl
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank.
Nucleic Acids Res.
David Sehnal, Radka Svobodová Vareková, Lukás Pravda, Crina-Maria Ionescu, Stanislav Geidl, Vladimír Horský, Deepti Jaiswal Kundu, Michaela Wimmerová, Jaroslav Koca
2014 J jnl
Anatomy of enzyme channels.
BMC Bioinform.
Lukás Pravda, Karel Berka, Radka Svobodová Vareková, David Sehnal, Pavel Banás, Roman A. Laskowski, Jaroslav Koca, Michal Otyepka
2014 J jnl
MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes.
Nucleic Acids Res.
Radka Svobodová Vareková, Deepti Jaiswal Kundu, David Sehnal, Crina-Maria Ionescu, Stanislav Geidl, Lukás Pravda, Vladimír Horský, Michaela Wimmerová, Jaroslav Koca
2013 J jnl
MOLE 2.0: advanced approach for analysis of biomacromolecular channels.
J. Cheminformatics
David Sehnal, Radka Svobodová Vareková, Karel Berka, Lukás Pravda, Veronika Navrátilová, Pavel Banás, Crina-Maria Ionescu, Michal Otyepka, Jaroslav Koca