David Hoksza

According to our database, David Hoksza authored at least 69 papers between 2007 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Visualizations for universal deep-feature representations: survey and taxonomy.

Tomás Skopal, Ladislav Peska, David Hoksza, Ivaná Sixtova, David Bernhauer

Knowl. Inf. Syst., February, 2024

2023

Visualization of automatically combined disease maps and pathway diagrams for rare diseases.

Piotr Gawron, David Hoksza, Janet Piñero, María Peña-Chilet, Marina Esteban-Medina, Jose Luis Fernandez-Rueda, Vincenza Colonna, Ewa Smula, Laurent Heirendt, François Ancien, Valentin Grouès, Venkata P. Satagopam, Reinhard Schneider, Joaquín Dopazo, Laura I. Furlong, Marek Ostaszewski

Frontiers Bioinform., May, 2023

Visual Representations for Data Analytics: User Study.

Ladislav Peska, Ivaná Sixtova, David Hoksza, David Bernhauer, Tomás Skopal

Proceedings of the Computer-Human Interaction Research and Applications, 2023

Cryptic binding site prediction with protein language models.

Vít Skrhak, Kamila Riedlova, Marian Novotny, David Hoksza

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

Framework for Protein Structures Conformation Analysis.

Vít Skrhak, David Hoksza

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

2022

AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands.

Christos P. Feidakis, Radoslav Krivák, David Hoksza, Marian Novotny

Bioinform., December, 2022

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, 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

Nucleic Acids Res., 2022

PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures.

David Jakubec, Petr Skoda, Radoslav Krivák, Marian Novotny, David Hoksza

Nucleic Acids Res., 2022

Machine and human interpretable patient visualizations.

Ivaná Sixtova, Tomás Skopal, David Hoksza, Jakub Matejík, Tomás Uher

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

Exploration of protein sequence embeddings for protein-ligand binding site detection.

David Hoksza, Hamza Gamouh

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2022

2021

Machine Learning to Support the Presentation of Complex Pathway Graphs.

Sune S. Nielsen, Marek Ostaszewski, Fintan McGee, David Hoksza, Simone Zorzan

IEEE ACM Trans. Comput. Biol. Bioinform., 2021

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases.

Blake A. Sweeney, Anton I. Petrov, Carlos Eduardo Ribas, Robert D. Finn, Alex Bateman, Maciej Szymanski, Wojciech M. Karlowski, Stefan E. Seemann, Jan Gorodkin, Jamie J. Cannone, Robin Ray Gutell, Simon Kay, Steven J. Marygold, Gilberto dos Santos, Adam Frankish, Jonathan M. Mudge, Ruth Barshir, Simon Fishilevich, Patricia P. Chan, Todd M. Lowe, Ruth L. Seal, Elspeth A. Bruford, Simona Panni, Pablo Porras, Dimitra Karagkouni, Artemis G. Hatzigeorgiou, Lina Ma, Zhang Zhang, Pieter-Jan Volders, Pieter Mestdagh, Sam Griffiths-Jones, Bastian Fromm, Kevin J. Peterson, Ioanna Kalvari, Eric P. Nawrocki, Anton S. Petrov, Shuai Weng, Philia Bouchard-Bourelle, Michelle S. Scott, Lauren M. Lui, David Hoksza, Ruth C. Lovering, Barbara Kramarz, Prita Mani, Sridhar Ramachandran, Zasha Weinberg

Nucleic Acids Res., 2021

Closing the gap between formats for storing layout information in systems biology.

David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider

Briefings Bioinform., 2021

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, 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

Nucleic Acids Res., 2020

MISCAST: MIssense variant to protein StruCture Analysis web SuiTe.

Sumaiya Iqbal, David Hoksza, Eduardo Pérez-Palma, Patrick May, Jakob B. Jespersen, Shehab S. Ahmed, Zaara T. Rifat, Henrike O. Heyne, Mohammad Sohel Rahman, Jeffrey R. Cottrell, Florence F. Wagner, Mark J. Daly, Arthur J. Campbell, Dennis Lal

Nucleic Acids Res., 2020

2019

PrankWeb: a web server for ligand binding site prediction and visualization.

Lukás Jendele, Radoslav Krivák, Petr Skoda, Marian Novotny, David Hoksza

Nucleic Acids Res., 2019

MINERVA API and plugins: opening molecular network analysis and visualization to the community.

David Hoksza, Piotr Gawron, Marek Ostaszewski, Ewa Smula, Reinhard Schneider

Bioinform., 2019

rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots.

Jan Jelínek, David Hoksza, Jan Hajic, Jan Pesek, Jan Drozen, Tomás Hladík, Michal Klimpera, Jirí Vohradský, Josef Pánek

Database J. Biol. Databases Curation, 2019

2018

P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure.

Radoslav Krivák, David Hoksza

J. Cheminformatics, 2018

MolArt: a molecular structure annotation and visualization tool.

David Hoksza, Piotr Gawron, Marek Ostaszewski, Reinhard Schneider

Bioinform., 2018

Software framework for similarity-based prediction of protein interfaces.

Jan Jelínek, Petr Skoda, David Hoksza

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

Peptide-Binding Site Prediction From Protein Structure via points on the Solvent Accessible Surface.

Radoslav Krivák, Lukás Jendele, David Hoksza

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2017

Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites.

Jan Jelínek, Petr Skoda, David Hoksza

BMC Bioinform., 2017

TRAVeLer: a tool for template-based RNA secondary structure visualization.

Richard Elias, David Hoksza

BMC Bioinform., 2017

Platform for ligand-based virtual screening integration.

Petr Skoda, David Hoksza, Jan Jelínek

Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

Improving quality of ligand-binding site prediction with Bayesian optimization.

Radoslav Krivák, David Hoksza, Petr Skoda

Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

Template-based prediction of RNA tertiary structure using its predicted secondary structure.

Rastislav Galvanek, David Hoksza

Proceedings of the 2017 IEEE International Conference on Bioinformatics and Biomedicine, 2017

2016

Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization.

Jakub Velkoborsky, David Hoksza

J. Cheminformatics, 2016

Using Bayesian modeling on molecular fragments features for virtual screening.

David Hoksza, Petr Skoda

Proceedings of the 2016 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2016

Benchmarking platform for ligand-based virtual screening.

Petr Skoda, David Hoksza

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

Template-based prediction of RNA tertiary structure.

Rastislav Galvanek, David Hoksza, Josef Pánek

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2016

2015

Multiple 3D RNA Structure Superposition Using Neighbor Joining.

David Hoksza, Daniel Svozil

IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features.

Radoslav Krivák, David Hoksza

J. Cheminformatics, 2015

MultiSETTER: web server for multiple RNA structure comparison.

Petr Cech, David Hoksza, Daniel Svozil

BMC Bioinform., 2015

Using Neo4j for Mining Protein Graphs: A Case Study.

David Hoksza, Jan Jelínek

Proceedings of the 26th International Workshop on Database and Expert Systems Applications, 2015

Activity-driven exploration of chemical space with morphing.

Martin Sícho, Daniel Svozil, David Hoksza

Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

Exploration of topological torsion fingerprints.

Petr Skoda, David Hoksza

Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015

P2RANK: Knowledge-Based Ligand Binding Site Prediction Using Aggregated Local Features.

Radoslav Krivák, David Hoksza

Proceedings of the Algorithms for Computational Biology, 2015

2014

Molpher: a software framework for systematic chemical space exploration.

David Hoksza, Petr Skoda, Milan Vorsilák, Daniel Svozil

J. Cheminformatics, 2014

2D Pharmacophore Query Generation.

David Hoksza, Petr Skoda

Proceedings of the Bioinformatics Research and Applications - 10th International Symposium, 2014

Template-based prediction of ribosomal RNA secondary structure.

Josef Pánek, Jan Hajic, David Hoksza

Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

Scaffold-based chemical space exploration.

David Hoksza, Petr Skoda

Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine, 2014

2013

On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications.

Jirí Novák, Timo Sachsenberg, David Hoksza, Tomás Skopal, Oliver Kohlbacher

J. Integr. Bioinform., 2013

MultiSETTER - Multiple RNA Structure Similarity Algorithm.

David Hoksza, Peter Szépe, Daniel Svozil

Proceedings of the Advances in Bioinformatics and Computational Biology, 2013

A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools.

Jirí Novák, Timo Sachsenberg, David Hoksza, Tomás Skopal, Oliver Kohlbacher

Proceedings of the 7th International Conference on Practical Applications of Computational Biology & Bioinformatics, 2013

Chemical space visualization using ViFrame.

Petr Skoda, David Hoksza

Proceedings of the 2013 IEEE/ACIS 12th International Conference on Computer and Information Science, 2013

2012

SETTER: web server for RNA structure comparison.

Petr Cech, Daniel Svozil, David Hoksza

Nucleic Acids Res., 2012

Non-metric similarity search of tandem mass spectra including posttranslational modifications.

Jirí Novák, Tomás Skopal, David Hoksza, Jakub Lokoc

J. Discrete Algorithms, 2012

Efficient RNA pairwise structure comparison by SETTER method.

David Hoksza, Daniel Svozil

Bioinform., 2012

SimTandem: Similarity Search in Tandem Mass Spectra.

Jirí Novák, Jakub Galgonek, David Hoksza, Tomás Skopal

Proceedings of the Similarity Search and Applications - 5th International Conference, 2012

On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering.

Jirí Novák, David Hoksza, Jakub Lokoc, Tomás Skopal

Proceedings of the Bioinformatics Research and Applications - 8th International Symposium, 2012

P3S: Protein Structure Similarity Search.

Jakub Galgonek, Tomás Skopal, David Hoksza

Proceedings of the Euro-Par 2012: Parallel Processing Workshops, 2012

On the Parallelization of the SProt Measure and the TM-Score Algorithm.

Jakub Galgonek, Martin Krulis, David Hoksza

Proceedings of the Euro-Par 2012: Parallel Processing Workshops, 2012

2011

Protein sequences identification using NM-tree.

Jirí Novák, Tomás Skopal, David Hoksza, Jakub Lokoc, Jakub Galgonek

Proceedings of the Fourth International Conference on Similarity Search and Applications, 2011

On metric approximations of the SProt measure.

Jakub Galgonek, David Hoksza

Proceedings of the Fourth International Conference on Similarity Search and Applications, 2011

SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm.

David Hoksza, Daniel Svozil

Proceedings of the Bioinformatics Research and Applications - 7th International Symposium, 2011

Exploration of Chemical Space by Molecular Morphing.

David Hoksza, Daniel Svozil

Proceedings of the 11th IEEE International Conference on Bioinformatics and Bioengineering, 2011

2010

Improving the similarity search of tandem mass spectra using metric access methods.

Jirí Novák, Tomás Skopal, David Hoksza, Jakub Lokoc

Proceedings of the Third International Workshop on Similarity Search and Applications, 2010

Parametrised Hausdorff Distance as a Non-Metric Similarity Model for Tandem Mass Spectrometry.

Jirí Novák, David Hoksza

Proceedings of the Dateso 2010 Annual International Workshop on DAtabases, 2010

Similarity search and posttranslational modifications in tandem mass spectra.

Jirí Novák, David Hoksza

Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2010

SProt - from local to global protein structure similarity.

Jakub Galgonek, David Hoksza

Proceedings of the 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2010

2009

On the Effectiveness of Distances Measuring Protein Structure Similarity.

Jakub Galgonek, David Hoksza

Proceedings of the Second International Workshop on Similarity Search and Applications, 2009

An application of the metric access methods to the mass spectrometry data.

Jirí Novák, David Hoksza

Proceedings of the 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2009

DDPIn - Distance and density based protein indexing.

David Hoksza

Proceedings of the 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2009

2008

Improved Alignment of Protein Sequences Based on Common Parts.

David Hoksza

Proceedings of the Bioinformatics Research and Applications, 2008

Native Multidimensional Indexing in Relational Databases.

David Hoksza, Tomás Skopal

Proceedings of the 14th International Conference on Management of Data, 2008

2007

Index-Based Approach to Similarity Search in Protein and Nucleotide Databases.

David Hoksza, Tomás Skopal

Proceedings of the Dateso 2007 Annual International Workshop on DAtabases, 2007

Construction of Tree-Based Indexes for Level-Contiguous Buffering Support.

Tomás Skopal, David Hoksza, Jaroslav Pokorný

Proceedings of the Advances in Databases: Concepts, 2007

Improving the Performance of M-Tree Family by Nearest-Neighbor Graphs.

Tomás Skopal, David Hoksza

Proceedings of the Advances in Databases and Information Systems, 2007