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Lukás Pravda
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2020 – today
- 2023
- [j15]Ibrahim Roshan Kunnakkattu, Preeti Choudhary
, Lukás Pravda, Nurul Nadzirin, Oliver S. Smart, Qi Yuan, Stephen Anyango, Sreenath Nair, Mihaly Varadi
, Sameer Velankar
:
PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank. J. Cheminformatics 15(1): 117 (2023) - 2022
- [j14]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
:
PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Res. 50(D1): 534-542 (2022) - 2021
- [j13]Sreenath Nair
, Mihaly Varadi
, Nurul Nadzirin, Lukás Pravda
, Stephen Anyango
, Saqib Mir, John M. Berrisford, David R. Armstrong
, Aleksandras Gutmanas
, Sameer Velankar
:
PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data. Bioinform. 37(21): 3950-3952 (2021) - [j12]Glen van Ginkel
, Lukás Pravda, Jose M. Dana, Mihaly Varadi
, Peter A. Keller, Stephen Anyango
, Sameer Velankar
:
PDBeCIF: an open-source mmCIF/CIF parsing and processing package. BMC Bioinform. 22(1): 383 (2021) - 2020
- [j11]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
:
PDBe: improved findability of macromolecular structure data in the PDB. Nucleic Acids Res. 48(Database-Issue): D335-D343 (2020) - [j10]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
:
PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 48(Database-Issue): D344-D353 (2020)
2010 – 2019
- 2019
- [j9]Abhik Mukhopadhyay
, Neera Borkakoti
, Lukás Pravda
, Jonathan D. Tyzack
, Janet M. Thornton
, Sameer Velankar
:
Finding enzyme cofactors in Protein Data Bank. Bioinform. 35(18): 3510-3511 (2019) - 2018
- [j8]Lukás Pravda
, David Sehnal, Radka Svobodová Vareková
, Veronika Navrátilová, Dominik Tousek, Karel Berka
, Michal Otyepka
, Jaroslav Koca
:
ChannelsDB: database of biomacromolecular tunnels and pores. Nucleic Acids Res. 46(Database-Issue): D399-D405 (2018) - [j7]Lukás Pravda
, David Sehnal, Dominik Tousek, Veronika Navrátilová, Václav Bazgier, Karel Berka
, Radka Svobodová Vareková
, Jaroslav Koca, Michal Otyepka
:
MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Res. 46(Webserver-Issue): W368-W373 (2018) - 2015
- [j6]Crina-Maria Ionescu, David Sehnal
, Francesco L. Falginella, Purbaj Pant
, Lukás Pravda
, Tomás Bouchal, Radka Svobodová Vareková
, Stanislav Geidl, Jaroslav Koca
:
AtomicChargeCalculator: interactive web-based calculation of atomic charges in large biomolecular complexes and drug-like molecules. J. Cheminformatics 7: 50:1-50:13 (2015) - [j5]David Sehnal
, Radka Svobodová Vareková
, Lukás Pravda
, Crina-Maria Ionescu, Stanislav Geidl, Vladimír Horský
, Deepti Jaiswal Kundu
, Michaela Wimmerová
, Jaroslav Koca
:
ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank. Nucleic Acids Res. 43(Database-Issue): 369-375 (2015) - [j4]David Sehnal
, Lukás Pravda
, Radka Svobodová Vareková
, Crina-Maria Ionescu, Jaroslav Koca
:
PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank. Nucleic Acids Res. 43(Webserver-Issue): W383-W388 (2015) - 2014
- [j3]Lukás Pravda
, Karel Berka
, Radka Svobodová Vareková
, David Sehnal
, Pavel Banás, Roman A. Laskowski
, Jaroslav Koca
, Michal Otyepka
:
Anatomy of enzyme channels. BMC Bioinform. 15: 379 (2014) - [j2]Radka Svobodová Vareková
, Deepti Jaiswal Kundu
, David Sehnal
, Crina-Maria Ionescu, Stanislav Geidl, Lukás Pravda
, Vladimír Horský
, Michaela Wimmerová
, Jaroslav Koca
:
MotiveValidator: interactive web-based validation of ligand and residue structure in biomolecular complexes. Nucleic Acids Res. 42(Webserver-Issue): 227-233 (2014) - 2013
- [j1]David Sehnal, Radka Svobodová Vareková, Karel Berka, Lukás Pravda, Veronika Navrátilová, Pavel Banás, Crina-Maria Ionescu, Michal Otyepka, Jaroslav Koca:
MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J. Cheminformatics 5: 39 (2013)
Coauthor Index
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