Improving the Performance of M-Tree Family by Nearest-Neighbor Graphs. - Tomás Skopal; David Hoksza (ADBIS, 2007)

Construction of Tree-Based Indexes for Level-Contiguous Buffering Support. - Tomás Skopal; David Hoksza; Jaroslav Pokorný (DASFAA, 2007)

Index-Based Approach to Similarity Search in Protein and Nucleotide Databases. - David Hoksza; Tomás Skopal (DATESO, 2007)

Native Multidimensional Indexing in Relational Databases. - David Hoksza; Tomás Skopal (COMAD, 2008)

Improved Alignment of Protein Sequences Based on Common Parts. - David Hoksza (ISBRA, 2008)

DDPIn - Distance and density based protein indexing. - David Hoksza (CIBCB, 2009)

An application of the metric access methods to the mass spectrometry data. - Jirí Novák; David Hoksza (CIBCB, 2009)

On the Effectiveness of Distances Measuring Protein Structure Similarity. - Jakub Galgonek; David Hoksza (SISAP, 2009)

SProt - from local to global protein structure similarity. - Jakub Galgonek; David Hoksza (BIBM Workshops, 2010)

Similarity search and posttranslational modifications in tandem mass spectra. - Jirí Novák; David Hoksza (BIBM Workshops, 2010)

Parametrised Hausdorff Distance as a Non-Metric Similarity Model for Tandem Mass Spectrometry. - Jirí Novák; David Hoksza (DATESO, 2010)

Improving the similarity search of tandem mass spectra using metric access methods. - Jirí Novák; Tomás Skopal; David Hoksza; Jakub Lokoc (SISAP, 2010)

Exploration of Chemical Space by Molecular Morphing. - David Hoksza; Daniel Svozil (BIBE, 2011)

SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm. - David Hoksza; Daniel Svozil (ISBRA, 2011)

On metric approximations of the SProt measure. - Jakub Galgonek; David Hoksza (SISAP, 2011)

Protein sequences identification using NM-tree. - Jirí Novák; Tomás Skopal; David Hoksza; Jakub Lokoc; Jakub Galgonek (SISAP, 2011)

On the Parallelization of the SProt Measure and the TM-Score Algorithm. - Jakub Galgonek; Martin Krulis; David Hoksza (Euro-Par Workshops, 2012)

P3S: Protein Structure Similarity Search. - Jakub Galgonek; Tomás Skopal; David Hoksza (Euro-Par Workshops, 2012)

On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering. - Jirí Novák; David Hoksza; Jakub Lokoc; Tomás Skopal (ISBRA, 2012)

SimTandem: Similarity Search in Tandem Mass Spectra. - Jirí Novák; Jakub Galgonek; David Hoksza; Tomás Skopal (SISAP, 2012)

Efficient RNA pairwise structure comparison by SETTER method. - David Hoksza; Daniel Svozil (Bioinform., 2012)

Non-metric similarity search of tandem mass spectra including posttranslational modifications. - Jirí Novák; Tomás Skopal; David Hoksza; Jakub Lokoc (J. Discrete Algorithms, 2012)

SETTER: web server for RNA structure comparison. - Petr Cech; Daniel Svozil; David Hoksza (Nucleic Acids Res., 2012)

Chemical space visualization using ViFrame. - Petr Skoda 001; David Hoksza (ICIS, 2013)

A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools. - Jirí Novák; Timo Sachsenberg; David Hoksza; Tomás Skopal; Oliver Kohlbacher (PACBB, 2013)

MultiSETTER - Multiple RNA Structure Similarity Algorithm. - David Hoksza; Peter Szépe; Daniel Svozil (BSB, 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)

Scaffold-based chemical space exploration. - David Hoksza; Petr Skoda 001 (BIBM, 2014)

Template-based prediction of ribosomal RNA secondary structure. - Josef Pánek; Jan Hajic Jr.; David Hoksza (BIBM, 2014)

2D Pharmacophore Query Generation. - David Hoksza; Petr Skoda 001 (ISBRA, 2014)

Molpher: a software framework for systematic chemical space exploration. - David Hoksza; Petr Skoda 001; Milan Vorsilák; Daniel Svozil (J. Cheminformatics, 2014)

P2RANK: Knowledge-Based Ligand Binding Site Prediction Using Aggregated Local Features. - Radoslav Krivák; David Hoksza (AlCoB, 2015)

Exploration of topological torsion fingerprints. - Petr Skoda 001; David Hoksza (BIBM, 2015)

Activity-driven exploration of chemical space with morphing. - Martin Sícho; Daniel Svozil; David Hoksza (BIBM, 2015)

Using Neo4j for Mining Protein Graphs: A Case Study. - David Hoksza; Jan Jelínek (DEXA Workshops, 2015)

MultiSETTER: web server for multiple RNA structure comparison. - Petr Cech; David Hoksza; Daniel Svozil (BMC 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)

Multiple 3D RNA Structure Superposition Using Neighbor Joining. - David Hoksza; Daniel Svozil (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Template-based prediction of RNA tertiary structure. - Rastislav Galvanek; David Hoksza; Josef Pánek (BIBM, 2016)

Benchmarking platform for ligand-based virtual screening. - Petr Skoda 001; David Hoksza (BIBM, 2016)

Using Bayesian modeling on molecular fragments features for virtual screening. - David Hoksza; Petr Skoda 001 (CIBCB, 2016)

Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization. - Jakub Velkoborsky; David Hoksza (J. Cheminformatics, 2016)

Template-based prediction of RNA tertiary structure using its predicted secondary structure. - Rastislav Galvanek; David Hoksza (BIBM, 2017)

Improving quality of ligand-binding site prediction with Bayesian optimization. - Radoslav Krivák; David Hoksza; Petr Skoda 001 (BIBM, 2017)

Platform for ligand-based virtual screening integration. - Petr Skoda 001; David Hoksza; Jan Jelínek (BIBM, 2017)

TRAVeLer: a tool for template-based RNA secondary structure visualization. - Richard Elias; David Hoksza (BMC Bioinform., 2017)

Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites. - Jan Jelínek; Petr Skoda 001; David Hoksza (BMC Bioinform., 2017)

Peptide-Binding Site Prediction From Protein Structure via points on the Solvent Accessible Surface. - Radoslav Krivák; Lukás Jendele; David Hoksza (BCB, 2018)

Software framework for similarity-based prediction of protein interfaces. - Jan Jelínek; Petr Skoda 001; David Hoksza (BIBM, 2018)

MolArt: a molecular structure annotation and visualization tool. - David Hoksza; Piotr Gawron; Marek Ostaszewski; Reinhard Schneider 002 (Bioinform., 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)

rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots. - Jan Jelínek; David Hoksza; Jan Hajic Jr.; Jan Pesek; Jan Drozen; Tomás Hladík; Michal Klimpera; Jirí Vohradský; Josef Pánek (Database J. Biol. Databases Curation, 2019)

MINERVA API and plugins: opening molecular network analysis and visualization to the community. - David Hoksza; Piotr Gawron; Marek Ostaszewski; Ewa Smula; Reinhard Schneider 002 (Bioinform., 2019)

PrankWeb: a web server for ligand binding site prediction and visualization. - Lukás Jendele; Radoslav Krivák; Petr Skoda 001; Marian Novotny; David Hoksza (Nucleic Acids Res., 2019)

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; et al. (Nucleic Acids Res., 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; et al. (Nucleic Acids Res., 2020)

Closing the gap between formats for storing layout information in systems biology. - David Hoksza; Piotr Gawron; Marek Ostaszewski; Jan Hasenauer; Reinhard Schneider 002 (Briefings 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; et al. (Nucleic Acids Res., 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)

Exploration of protein sequence embeddings for protein-ligand binding site detection. - David Hoksza; Hamza Gamouh (BIBM, 2022)

Machine and human interpretable patient visualizations. - Ivaná Sixtova; Tomás Skopal; David Hoksza; Jakub Matejík; Tomás Uher (BIBM, 2022)

PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures. - David Jakubec; Petr Skoda 001; Radoslav Krivák; Marian Novotny; David Hoksza (Nucleic Acids Res., 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; et al. (Nucleic Acids Res., 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., 2022)

Framework for Protein Structures Conformation Analysis. - Vít Skrhak; David Hoksza (BIBM, 2023)

Cryptic binding site prediction with protein language models. - Vít Skrhak; Kamila Riedlova; Marian Novotny; David Hoksza (BIBM, 2023)

Visual Representations for Data Analytics: User Study. - Ladislav Peska; Ivaná Sixtova; David Hoksza; David Bernhauer; Tomás Skopal (CHIRA (2), 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; et al. (Frontiers Bioinform., 2023)

Integrating Structural Features with Protein Language Models to Predict Protein-Ligand Binding Sites. - Matyás Brabec; David Hoksza (BIBM, 2024)

Protein Family Sequence Generation Through ProGen2 Fine-Tuning. - Hugo Hrbán; David Hoksza (BIBM, 2024)

Visualizations for universal deep-feature representations: survey and taxonomy. - Tomás Skopal; Ladislav Peska; David Hoksza; Ivaná Sixtova; David Bernhauer (Knowl. Inf. Syst., 2024)

Unified Visual-Aware Representations for Data Analytics. - Ladislav Peska; Ivaná Sixtova; David Hoksza; David Bernhauer; Jakub Lokoc; Tomás Skopal (IEEE Access, 2025)