David Hoksza - RankMe

80 papers B 6C 6Misc 2Journal 30Unranked 36

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	Beyond Exact Matches: Near-Hit Scoring for Protein Binding Site Prediction with Protein Language Models. BIBM Yana Podlesna, Vít Skrhák, David Hoksza
2025	J	`jnl`	CryptoBench: cryptic protein-ligand binding sites dataset and benchmark. Bioinform. Vít Skrhák, Marián Novotný, Christos P. Feidakis, Radoslav Krivák, David Hoksza
2025	—	`conf`	Hidden in protein sequences: Predicting cryptic binding sites. BCB Vít Skrhák, Hamza Gamouh, David Hoksza
2025	J	`jnl`	Hybrid protein-ligand binding residue prediction with protein language models: does the structure matter? Bioinform. Hamza Gamouh, Marián Novotný, David Hoksza
2025	J	`jnl`	Unified Visual-Aware Representations for Data Analytics. IEEE Access Ladislav Peska, Ivaná Sixtova, David Hoksza, David Bernhauer, Jakub Lokoc, Tomás Skopal
2024	—	`conf`	Integrating Structural Features with Protein Language Models to Predict Protein-Ligand Binding Sites. BIBM Matyás Brabec, David Hoksza
2024	—	`conf`	Protein Family Sequence Generation Through ProGen2 Fine-Tuning. BIBM Hugo Hrbán, David Hoksza
2024	—	`conf`	Protein Family Sequence Generation through ProGen2 Fine-Tuning. BIBM Hugo Hrbán, David Hoksza
2024	—	`conf`	Protein Family Sequence Generation through ProGen2 Fine-Tuning. BIBM Hugo Hrbán, David Hoksza
2024	J	`jnl`	Visualizations for universal deep-feature representations: survey and taxonomy. Knowl. Inf. Syst. Tomás Skopal, Ladislav Peska, David Hoksza, Ivaná Sixtova, David Bernhauer
2023	—	`conf`	Cryptic binding site prediction with protein language models. BIBM Vít Skrhák, Kamila Riedlova, Marian Novotny, David Hoksza
2023	—	`conf`	Framework for Protein Structures Conformation Analysis. BIBM Vít Skrhák, David Hoksza
2023	—	`conf`	Visual Representations for Data Analytics: User Study. CHIRA (2) Ladislav Peska, Ivaná Sixtova, David Hoksza, David Bernhauer, Tomás Skopal
2023	J	`jnl`	Visualization of automatically combined disease maps and pathway diagrams for rare diseases. Frontiers Bioinform. 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
2022	J	`jnl`	AHoJ: rapid, tailored search and retrieval of apo and holo protein structures for user-defined ligands. Bioinform. Christos P. Feidakis, Radoslav Krivák, David Hoksza, Marian Novotny
2022	—	`conf`	Exploration of protein sequence embeddings for protein-ligand binding site detection. BIBM David Hoksza, Hamza Gamouh
2022	—	`conf`	Machine and human interpretable patient visualizations. BIBM Ivaná Sixtova, Tomás Skopal, David Hoksza, Jakub Matejík, Tomás Uher
2022	J	`jnl`	PDBe-KB: collaboratively defining the biological context of structural data. Nucleic Acids Res. 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
2022	J	`jnl`	PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures. Nucleic Acids Res. David Jakubec, Petr Skoda, Radoslav Krivák, Marian Novotny, David Hoksza
2021	J	`jnl`	Closing the gap between formats for storing layout information in systems biology. Briefings Bioinform. David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider
2021	J	`jnl`	Machine Learning to Support the Presentation of Complex Pathway Graphs. IEEE ACM Trans. Comput. Biol. Bioinform. Sune S. Nielsen, Marek Ostaszewski, Fintan McGee, David Hoksza, Simone Zorzan
2021	J	`jnl`	RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res. 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
2020	J	`jnl`	Closing the gap between formats for storing layout information in systems biology. Briefings Bioinform. David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider
2020	J	`jnl`	MISCAST: MIssense variant to protein StruCture Analysis web SuiTe. Nucleic Acids Res. 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
2020	J	`jnl`	PDBe-KB: a community-driven resource for structural and functional annotations. Nucleic Acids Res. 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
2019	J	`jnl`	MINERVA API and plugins: opening molecular network analysis and visualization to the community. Bioinform. David Hoksza, Piotr Gawron, Marek Ostaszewski, Ewa Smula, Reinhard Schneider
2019	J	`jnl`	PrankWeb: a web server for ligand binding site prediction and visualization. Nucleic Acids Res. Lukás Jendele, Radoslav Krivák, Petr Skoda, Marian Novotny, David Hoksza
2019	J	`jnl`	rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots. Database J. Biol. Databases Curation Jan Jelínek, David Hoksza, Jan Hajic, Jan Pesek, Jan Drozen, Tomás Hladík, Michal Klimpera, Jirí Vohradský, Josef Pánek
2018	J	`jnl`	MolArt: a molecular structure annotation and visualization tool. Bioinform. David Hoksza, Piotr Gawron, Marek Ostaszewski, Reinhard Schneider
2018	J	`jnl`	P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure. J. Cheminformatics Radoslav Krivák, David Hoksza
2018	—	`conf`	Peptide-Binding Site Prediction From Protein Structure via points on the Solvent Accessible Surface. BCB Radoslav Krivák, Lukás Jendele, David Hoksza
2018	—	`conf`	Software framework for similarity-based prediction of protein interfaces. BIBM Jan Jelínek, Petr Skoda, David Hoksza
2017	—	`conf`	Improving quality of ligand-binding site prediction with Bayesian optimization. BIBM Radoslav Krivák, David Hoksza, Petr Skoda
2017	—	`conf`	Platform for ligand-based virtual screening integration. BIBM Petr Skoda, David Hoksza, Jan Jelínek
2017	J	`jnl`	TRAVeLer: a tool for template-based RNA secondary structure visualization. BMC Bioinform. Richard Elias, David Hoksza
2017	—	`conf`	Template-based prediction of RNA tertiary structure using its predicted secondary structure. BIBM Rastislav Galvanek, David Hoksza
2017	J	`jnl`	Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites. BMC Bioinform. Jan Jelínek, Petr Skoda, David Hoksza
2016	—	`conf`	Benchmarking platform for ligand-based virtual screening. BIBM Petr Skoda, David Hoksza
2016	J	`jnl`	Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization. J. Cheminformatics Jakub Velkoborsky, David Hoksza
2016	—	`conf`	Template-based prediction of RNA tertiary structure. BIBM Rastislav Galvanek, David Hoksza, Josef Pánek
2016	C	`conf`	Using Bayesian modeling on molecular fragments features for virtual screening. CIBCB David Hoksza, Petr Skoda
2016	—	`conf`	Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites. ICCABS Jan Jelínek, Petr Skoda, David Hoksza
2015	—	`conf`	Activity-driven exploration of chemical space with morphing. BIBM Martin Sícho, Daniel Svozil, David Hoksza
2015	—	`conf`	Exploration of topological torsion fingerprints. BIBM Petr Skoda, David Hoksza
2015	J	`jnl`	Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features. J. Cheminformatics Radoslav Krivák, David Hoksza
2015	J	`jnl`	MultiSETTER: web server for multiple RNA structure comparison. BMC Bioinform. Petr Cech, David Hoksza, Daniel Svozil
2015	J	`jnl`	Multiple 3D RNA Structure Superposition Using Neighbor Joining. IEEE ACM Trans. Comput. Biol. Bioinform. David Hoksza, Daniel Svozil
2015	—	`conf`	P2RANK: Knowledge-Based Ligand Binding Site Prediction Using Aggregated Local Features. AlCoB Radoslav Krivák, David Hoksza
2015	—	`conf`	Using Neo4j for Mining Protein Graphs: A Case Study. DEXA Workshops David Hoksza, Jan Jelínek
2014	—	`conf`	2D Pharmacophore Query Generation. ISBRA David Hoksza, Petr Skoda
2014	J	`jnl`	Molpher: a software framework for systematic chemical space exploration. J. Cheminformatics David Hoksza, Petr Skoda, Milan Vorsilák, Daniel Svozil
2014	—	`conf`	Scaffold-based chemical space exploration. BIBM David Hoksza, Petr Skoda
2014	—	`conf`	Template-based prediction of ribosomal RNA secondary structure. BIBM Josef Pánek, Jan Hajic Jr., David Hoksza
2013	Misc	`conf`	A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools. PACBB Jirí Novák, Timo Sachsenberg, David Hoksza, Tomás Skopal, Oliver Kohlbacher
2013	C	`conf`	Chemical space visualization using ViFrame. ICIS Petr Skoda, David Hoksza
2013	—	`conf`	MultiSETTER - Multiple RNA Structure Similarity Algorithm. BSB David Hoksza, Peter Szépe, Daniel Svozil
2013	J	`jnl`	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. Jirí Novák, Timo Sachsenberg, David Hoksza, Tomás Skopal, Oliver Kohlbacher
2012	J	`jnl`	Efficient RNA pairwise structure comparison by SETTER method. Bioinform. David Hoksza, Daniel Svozil
2012	J	`jnl`	Non-metric similarity search of tandem mass spectra including posttranslational modifications. J. Discrete Algorithms Jirí Novák, Tomás Skopal, David Hoksza, Jakub Lokoc
2012	—	`conf`	On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering. ISBRA Jirí Novák, David Hoksza, Jakub Lokoc, Tomás Skopal
2012	—	`conf`	On the Parallelization of the SProt Measure and the TM-Score Algorithm. Euro-Par Workshops Jakub Galgonek, Martin Krulis, David Hoksza
2012	—	`conf`	P3S: Protein Structure Similarity Search. Euro-Par Workshops Jakub Galgonek, Tomás Skopal, David Hoksza
2012	J	`jnl`	SETTER: web server for RNA structure comparison. Nucleic Acids Res. Petr Cech, Daniel Svozil, David Hoksza
2012	B	`conf`	SimTandem: Similarity Search in Tandem Mass Spectra. SISAP Jirí Novák, Jakub Galgonek, David Hoksza, Tomás Skopal
2011	C	`conf`	Exploration of Chemical Space by Molecular Morphing. BIBE David Hoksza, Daniel Svozil
2011	B	`conf`	On metric approximations of the SProt measure. SISAP Jakub Galgonek, David Hoksza
2011	B	`conf`	Protein sequences identification using NM-tree. SISAP Jirí Novák, Tomás Skopal, David Hoksza, Jakub Lokoc, Jakub Galgonek
2011	—	`conf`	SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm. ISBRA David Hoksza, Daniel Svozil
2010	B	`conf`	Improving the similarity search of tandem mass spectra using metric access methods. SISAP Jirí Novák, Tomás Skopal, David Hoksza, Jakub Lokoc
2010	—	`conf`	Parametrised Hausdorff Distance as a Non-Metric Similarity Model for Tandem Mass Spectrometry. DATESO Jirí Novák, David Hoksza
2010	—	`conf`	SProt - from local to global protein structure similarity. BIBM Workshops Jakub Galgonek, David Hoksza
2010	—	`conf`	Similarity search and posttranslational modifications in tandem mass spectra. BIBM Workshops Jirí Novák, David Hoksza
2009	C	`conf`	An application of the metric access methods to the mass spectrometry data. CIBCB Jirí Novák, David Hoksza
2009	C	`conf`	DDPIn - Distance and density based protein indexing. CIBCB David Hoksza
2009	B	`conf`	On the Effectiveness of Distances Measuring Protein Structure Similarity. SISAP Jakub Galgonek, David Hoksza
2008	—	`conf`	Improved Alignment of Protein Sequences Based on Common Parts. ISBRA David Hoksza
2008	Misc	`conf`	Native Multidimensional Indexing in Relational Databases. COMAD David Hoksza, Tomás Skopal
2007	B	`conf`	Construction of Tree-Based Indexes for Level-Contiguous Buffering Support. DASFAA Tomás Skopal, David Hoksza, Jaroslav Pokorný
2007	C	`conf`	Improving the Performance of M-Tree Family by Nearest-Neighbor Graphs. ADBIS Tomás Skopal, David Hoksza
2007	—	`conf`	Index-Based Approach to Similarity Search in Protein and Nucleotide Databases. DATESO David Hoksza, Tomás Skopal