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David Hoksza
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P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure
R Krivák, D Hoksza
Journal of cheminformatics 10, 1-12, 2018
4082018
PrankWeb: a web server for ligand binding site prediction and visualization
L Jendele, R Krivak, P Skoda, M Novotny, D Hoksza
Nucleic acids research 47 (W1), W345-W349, 2019
3352019
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases
Nucleic acids research 49 (D1), D212-D220, 2021
2412021
PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures
D Jakubec, P Skoda, R Krivak, M Novotny, D Hoksza
Nucleic Acids Research 50 (W1), W593-W597, 2022
1202022
R2DT is a framework for predicting and visualising RNA secondary structure using templates
BA Sweeney, D Hoksza, EP Nawrocki, CE Ribas, F Madeira, JJ Cannone, ...
Nature Communications 12 (1), 3494, 2021
932021
Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants
S Iqbal, E Pérez-Palma, JB Jespersen, P May, D Hoksza, HO Heyne, ...
Proceedings of the National Academy of Sciences 117 (45), 28201-28211, 2020
912020
PDBe-KB: a community-driven resource for structural and functional annotations
M Varadi, J Berrisford, M Deshpande, SS Nair, A Gutmanas, D Armstrong, ...
Nucleic Acids Research 48 (D1), D344-D353, 2020
842020
Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features
R Krivák, D Hoksza
Journal of cheminformatics 7, 1-13, 2015
782015
Molpher: a software framework for systematic chemical space exploration
D Hoksza, P Škoda, M Voršilák, D Svozil
Journal of cheminformatics 6, 1-13, 2014
472014
PDBe-KB: collaboratively defining the biological context of structural data
Nucleic acids research 50 (D1), D534-D542, 2022
422022
Efficient RNA pairwise structure comparison by SETTER method
D Hoksza, D Svozil
Bioinformatics 28 (14), 1858-1864, 2012
372012
SETTER: web server for RNA structure comparison
P Čech, D Svozil, D Hoksza
Nucleic acids research 40 (W1), W42-W48, 2012
352012
MINERVA API and plugins: opening molecular network analysis and visualization to the community
D Hoksza, P Gawron, M Ostaszewski, E Smula, R Schneider
Bioinformatics 35 (21), 4496-4498, 2019
342019
Improving the performance of M-tree family by nearest-neighbor graphs
T Skopal, D Hoksza
Advances in Databases and Information Systems: 11th East European Conference …, 2007
282007
MolArt: a molecular structure annotation and visualization tool
D Hoksza, P Gawron, M Ostaszewski, R Schneider
Bioinformatics 34 (23), 4127-4128, 2018
262018
TRAVeLer: a tool for template-based RNA secondary structure visualization
R Elias, D Hoksza
BMC bioinformatics 18, 1-10, 2017
262017
Using Neo4j for mining protein graphs: a case study
D Hoksza, J Jelínek
2015 26th International Workshop on Database and Expert Systems Applications …, 2015
222015
Closing the gap between formats for storing layout information in systems biology
D Hoksza, P Gawron, M Ostaszewski, J Hasenauer, R Schneider
Briefings in bioinformatics 21 (4), 1249-1260, 2020
212020
MISCAST: MIssense variant to protein StruCture Analysis web SuiTe
S Iqbal, D Hoksza, E Pérez-Palma, P May, JB Jespersen, SS Ahmed, ...
Nucleic Acids Research 48 (W1), W132-W139, 2020
192020
Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization
J Velkoborsky, D Hoksza
Journal of Cheminformatics 8, 1-14, 2016
192016
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Articles 1–20