David Hoksza

Publication Activity (10 Years)

Years Active: 2007-2024
Publications (10 Years): 40

Top Topics

Virtual Screening

Secondary Structure

Visual Representations

Top Venues

Nucleic Acids Res.

J. Cheminformatics

Publications

Tomás Skopal, Ladislav Peska, David Hoksza, Ivaná Sixtova, David Bernhauer
Visualizations for universal deep-feature representations: survey and taxonomy. Knowl. Inf. Syst. 66 (2) (2024)
Ladislav Peska, Ivaná Sixtova, David Hoksza, David Bernhauer, Tomás Skopal
Visual Representations for Data Analytics: User Study. CHIRA (2) (2023)
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
Visualization of automatically combined disease maps and pathway diagrams for rare diseases. Frontiers Bioinform. 3 (2023)
Vít Skrhak, David Hoksza
Framework for Protein Structures Conformation Analysis. BIBM (2023)
Vít Skrhak, Kamila Riedlova, Marian Novotny, David Hoksza
Cryptic binding site prediction with protein language models. BIBM (2023)
David Jakubec, Petr Skoda, Radoslav Krivák, Marian Novotny, David Hoksza
PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures. Nucleic Acids Res. 50 (W1) (2022)
David Hoksza, Hamza Gamouh
Exploration of protein sequence embeddings for protein-ligand binding site detection. BIBM (2022)
Christos P. Feidakis, Radoslav Krivák, David Hoksza, Marian Novotny
AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands. Bioinform. 38 (24) (2022)
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) (2022)
Ivaná Sixtova, Tomás Skopal, David Hoksza, Jakub Matejík, Tomás Uher
Machine and human interpretable patient visualizations. BIBM (2022)
Sune S. Nielsen, Marek Ostaszewski, Fintan McGee, David Hoksza, Simone Zorzan
Machine Learning to Support the Presentation of Complex Pathway Graphs. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (3) (2021)
David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider
Closing the gap between formats for storing layout information in systems biology. Briefings Bioinform. 22 (1) (2021)
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
RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res. 49 (Database-Issue) (2021)
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
MISCAST: MIssense variant to protein StruCture Analysis web SuiTe. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
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) (2020)
David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider
Closing the gap between formats for storing layout information in systems biology. Briefings Bioinform. 21 (4) (2020)
Jan Jelínek, David Hoksza, Jan Hajic, Jan Pesek, Jan Drozen, Tomás Hladík, Michal Klimpera, Jirí Vohradský, Josef Pánek
rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots. Database J. Biol. Databases Curation 2019 (2019)
Lukás Jendele, Radoslav Krivák, Petr Skoda, Marian Novotny, David Hoksza
PrankWeb: a web server for ligand binding site prediction and visualization. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
David Hoksza, Piotr Gawron, Marek Ostaszewski, Ewa Smula, Reinhard Schneider
MINERVA API and plugins: opening molecular network analysis and visualization to the community. Bioinform. 35 (21) (2019)
Jan Jelínek, Petr Skoda, David Hoksza
Software framework for similarity-based prediction of protein interfaces. BIBM (2018)
Radoslav Krivák, Lukás Jendele, David Hoksza
Peptide-Binding Site Prediction From Protein Structure via points on the Solvent Accessible Surface. BCB (2018)
David Hoksza, Piotr Gawron, Marek Ostaszewski, Reinhard Schneider
MolArt: a molecular structure annotation and visualization tool. Bioinform. 34 (23) (2018)
Radoslav Krivák, David Hoksza
P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure. J. Cheminformatics 10 (1) (2018)
Rastislav Galvanek, David Hoksza
Template-based prediction of RNA tertiary structure using its predicted secondary structure. BIBM (2017)
Petr Skoda, David Hoksza, Jan Jelínek
Platform for ligand-based virtual screening integration. BIBM (2017)
Radoslav Krivák, David Hoksza, Petr Skoda
Improving quality of ligand-binding site prediction with Bayesian optimization. BIBM (2017)
Jan Jelínek, Petr Skoda, David Hoksza
Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites. BMC Bioinform. 18 (15) (2017)
Richard Elias, David Hoksza
TRAVeLer: a tool for template-based RNA secondary structure visualization. BMC Bioinform. 18 (1) (2017)
Jakub Velkoborsky, David Hoksza
Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization. J. Cheminformatics 8 (1) (2016)
Petr Skoda, David Hoksza
Benchmarking platform for ligand-based virtual screening. BIBM (2016)
David Hoksza, Petr Skoda
Using Bayesian modeling on molecular fragments features for virtual screening. CIBCB (2016)
Rastislav Galvanek, David Hoksza, Josef Pánek
Template-based prediction of RNA tertiary structure. BIBM (2016)
Jan Jelínek, Petr Skoda, David Hoksza
Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites. ICCABS (2016)
Radoslav Krivák, David Hoksza
P2RANK: Knowledge-Based Ligand Binding Site Prediction Using Aggregated Local Features. AlCoB (2015)
Petr Cech, David Hoksza, Daniel Svozil
MultiSETTER: web server for multiple RNA structure comparison. BMC Bioinform. 16 (2015)
Radoslav Krivák, David Hoksza
Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features. J. Cheminformatics 7 (2015)
David Hoksza, Daniel Svozil
Multiple 3D RNA Structure Superposition Using Neighbor Joining. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (3) (2015)
David Hoksza, Jan Jelínek
Using Neo4j for Mining Protein Graphs: A Case Study. DEXA Workshops (2015)
Petr Skoda, David Hoksza
Exploration of topological torsion fingerprints. BIBM (2015)
Martin Sícho, Daniel Svozil, David Hoksza
Activity-driven exploration of chemical space with morphing. BIBM (2015)
David Hoksza, Petr Skoda, Milan Vorsilák, Daniel Svozil
Molpher: a software framework for systematic chemical space exploration. J. Cheminformatics 6 (1) (2014)
David Hoksza, Petr Skoda
2D Pharmacophore Query Generation. ISBRA (2014)
David Hoksza, Petr Skoda
Scaffold-based chemical space exploration. BIBM (2014)
Josef Pánek, Jan Hajic, David Hoksza
Template-based prediction of ribosomal RNA secondary structure. BIBM (2014)
Petr Skoda, David Hoksza
Chemical space visualization using ViFrame. ICIS (2013)
Jiri Novák, Timo Sachsenberg, David Hoksza, Tomás Skopal, Oliver Kohlbacher
On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications. J. Integr. Bioinform. 10 (3) (2013)
David Hoksza, Peter Szépe, Daniel Svozil
MultiSETTER - Multiple RNA Structure Similarity Algorithm. BSB (2013)
Jiri Novák, Timo Sachsenberg, David Hoksza, Tomás Skopal, Oliver Kohlbacher
A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools. PACBB (2013)
David Hoksza, Daniel Svozil
Efficient RNA pairwise structure comparison by SETTER method. Bioinform. 28 (14) (2012)
Jakub Galgonek, Martin Krulis, David Hoksza
On the Parallelization of the SProt Measure and the TM-Score Algorithm. Euro-Par Workshops (2012)
Jiri Novák, Jakub Galgonek, David Hoksza, Tomás Skopal
SimTandem: Similarity Search in Tandem Mass Spectra. SISAP (2012)
Petr Cech, Daniel Svozil, David Hoksza
SETTER: web server for RNA structure comparison. Nucleic Acids Res. 40 (Web-Server-Issue) (2012)
Jiri Novák, David Hoksza, Jakub Lokoc, Tomás Skopal
On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering. ISBRA (2012)
Jakub Galgonek, Tomás Skopal, David Hoksza
P3S: Protein Structure Similarity Search. Euro-Par Workshops (2012)
Jiri Novák, Tomás Skopal, David Hoksza, Jakub Lokoc
Non-metric similarity search of tandem mass spectra including posttranslational modifications. J. Discrete Algorithms 13 (2012)
David Hoksza, Daniel Svozil
Exploration of Chemical Space by Molecular Morphing. BIBE (2011)
David Hoksza, Daniel Svozil
SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm. ISBRA (2011)
Jiri Novák, Tomás Skopal, David Hoksza, Jakub Lokoc, Jakub Galgonek
Protein sequences identification using NM-tree. SISAP (2011)
Jakub Galgonek, David Hoksza
On metric approximations of the SProt measure. SISAP (2011)
Jiri Novák, Tomás Skopal, David Hoksza, Jakub Lokoc
Improving the similarity search of tandem mass spectra using metric access methods. SISAP (2010)
Jakub Galgonek, David Hoksza
SProt - from local to global protein structure similarity. BIBM Workshops (2010)
Jiri Novák, David Hoksza
Similarity search and posttranslational modifications in tandem mass spectra. BIBM Workshops (2010)
Jiri Novák, David Hoksza
Parametrised Hausdorff Distance as a Non-Metric Similarity Model for Tandem Mass Spectrometry. DATESO (2010)
Jakub Galgonek, David Hoksza
On the Effectiveness of Distances Measuring Protein Structure Similarity. SISAP (2009)
Jiri Novák, David Hoksza
An application of the metric access methods to the mass spectrometry data. CIBCB (2009)
David Hoksza
DDPIn - Distance and density based protein indexing. CIBCB (2009)
David Hoksza, Tomás Skopal
Native Multidimensional Indexing in Relational Databases. COMAD (2008)
David Hoksza
Improved Alignment of Protein Sequences Based on Common Parts. ISBRA (2008)
Tomás Skopal, David Hoksza, Jaroslav Pokorný
Construction of Tree-Based Indexes for Level-Contiguous Buffering Support. DASFAA (2007)
David Hoksza, Tomás Skopal
Index-Based Approach to Similarity Search in Protein and Nucleotide Databases. DATESO (2007)
Tomás Skopal, David Hoksza
Improving the Performance of M-Tree Family by Nearest-Neighbor Graphs. ADBIS (2007)