David Sehnal

Publication Activity (10 Years)

Years Active: 2011-2023
Publications (10 Years): 9

Top Topics

Structural Patterns

Top Venues

Nucleic Acids Res.

J. Cheminformatics

Publications

Adam Midlik, Sreenath Nair, Stephen Anyango, Mandar S. Deshpande, David Sehnal, Mihaly Varadi, Sameer Velankar
PDBImages: a command-line tool for automated macromolecular structure visualization. Bioinform. 39 (12) (2023)
Aliaksei Chareshneu, Adam Midlik, Crina-Maria Ionescu, Alexander S. Rose, Vladimír Horský, Alessio Cantara, Radka Svobodová Vareková, Karel Berka, David Sehnal
Mol* Volumes and Segmentations: visualization and interpretation of cell imaging data alongside macromolecular structure data and biological annotations. Nucleic Acids Res. 51 (W1) (2023)
David Sehnal, Sebastian Bittrich, Mandar S. Deshpande, Radka Svobodová, Karel Berka, Václav Bazgier, Sameer Velankar, Stephen K. Burley, Jaroslav Koca, Alexander S. Rose
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Res. 49 (Webserver-Issue) (2021)
David Sehnal, Sebastian Bittrich, Sameer Velankar, Jaroslav Koca, Radka Svobodová Vareková, Stephen K. Burley, Alexander S. Rose
BinaryCIF and CIFTools - Lightweight, efficient and extensible macromolecular data management. PLoS Comput. Biol. 16 (10) (2020)
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) (2020)
David Sehnal, Alexander S. Rose, Jaroslav Koca, Stephen K. Burley, Sameer Velankar
Mol*: Towards a Common Library and Tools for Web Molecular Graphics. MolVa@EuroVis (2018)
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, Lora Mak, Abhik Mukhopadhyay, Nurul Nadzirin, Typhaine Paysan-Lafosse, David Sehnal, Sanchayita Sen, Oliver S. Smart, Mihaly Varadi, Gerard J. Kleywegt, Sameer Velankar
PDBe: towards reusable data delivery infrastructure at protein data bank in Europe. Nucleic Acids Res. 46 (Database-Issue) (2018)
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) (2018)
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) (2018)
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) (2015)
Szymon Tengler, David Sehnal
Method of Solving the Volume Between Triangulated Mesh Surfaces. ISAT (3) (2015)
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) (2015)
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 (2015)
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) (2014)
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 (2014)
Deepti Jaiswal Kundu, David Sehnal, Radka Svobodová Vareková, Crina-Maria Ionescu, Jaroslav Koca
Consistency of sugar structures and their annotation in the PDB. J. Cheminformatics 6 (S-1) (2014)
Radka Svobodová Vareková, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Tomás Bouchal, David Sehnal, Ruben Abagyan, Jaroslav Koca
Predicting pKa values from EEM atomic charges. J. Cheminformatics 5 (2013)
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 (2013)
David Sehnal, Radka Svobodová Vareková, Heinrich J. Huber, Stanislav Geidl, Crina-Maria Ionescu, Michaela Wimmerová, Jaroslav Koca
SiteBinder: An Improved Approach for Comparing Multiple Protein Structural Motifs. J. Chem. Inf. Model. 52 (2) (2012)
Ondrej Skrehota, Radka Svobodová Vareková, Stanislav Geidl, Michal Kudera, David Sehnal, Crina-Maria Ionescu, Jan Zidek, Jaroslav Koca
QSPR designer - employ your own descriptors in the automated QSAR modeling process. J. Cheminformatics 4 (S-1) (2012)
Karel Berka, Ondrej Hanák, David Sehnal, Pavel Banás, Veronika Navrátilová, Deepti Jaiswal Kundu, Crina-Maria Ionescu, Radka Svobodová Vareková, Jaroslav Koca, Michal Otyepka
2.0: interactive web-based analysis of biomacromolecular channels. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Deepti Jaiswal Kundu, Radka Svobodová Vareková, Crina-Maria Ionescu, David Sehnal, Jaroslav Koca
Searching for tunnels of proteins - comparison of approaches and available software tools. J. Cheminformatics 4 (S-1) (2012)
David Sehnal, Radka Svobodová Vareková, Heinrich J. Huber, Stanislav Geidl, Crina-Maria Ionescu, Michaela Wimmerová, Jaroslav Koca
SiteBinder - an improved approach for comparing multiple protein structural motifs. Case studies on biologically important motifs. J. Cheminformatics 4 (S-1) (2012)
Ondrej Skrehota, Radka Svobodová Vareková, Stanislav Geidl, Michal Kudera, David Sehnal, Crina-Maria Ionescu, Jaroslav Koca
prediction. J. Cheminformatics 3 (S-1) (2011)
Radka Svobodová Vareková, Stanislav Geidl, Crina-Maria Ionescu, Ondrej Skrehota, Michal Kudera, David Sehnal, Tomás Bouchal, Ruben Abagyan, Heinrich J. Huber, Jaroslav Koca
Values of Substituted Phenols from Atomic Charges: Comparison of Different Quantum Mechanical Methods and Charge Distribution Schemes. J. Chem. Inf. Model. 51 (8) (2011)