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2020 – today
- 2024
[j27]Tomás Skopal
, Ladislav Peska, David Hoksza, Ivaná Sixtova, David Bernhauer:
Visualizations for universal deep-feature representations: survey and taxonomy. Knowl. Inf. Syst. 66(2): 811-840 (2024)- 2023
- [j26]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) - [c44]Vít Skrhak, Kamila Riedlova, Marian Novotny, David Hoksza:
Cryptic binding site prediction with protein language models. BIBM 2023: 2883-2888 - [c43]Vít Skrhak, David Hoksza:
Framework for Protein Structures Conformation Analysis. BIBM 2023: 4942-4944 - [c42]Ladislav Peska, Ivaná Sixtova, David Hoksza, David Bernhauer, Tomás Skopal:
Visual Representations for Data Analytics: User Study. CHIRA (2) 2023: 231-243 - 2022
- [j25]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): 5452-5453 (2022) - [j24]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): 534-542 (2022) - [j23]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): 593-597 (2022) - [c41]David Hoksza, Hamza Gamouh:
Exploration of protein sequence embeddings for protein-ligand binding site detection. BIBM 2022: 3356-3361 - [c40]Ivaná Sixtova, Tomás Skopal, David Hoksza, Jakub Matejík, Tomás Uher:
Machine and human interpretable patient visualizations. BIBM 2022: 3879-3881 - 2021
- [j22]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): 608 (2021) - [j21]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): D212-D220 (2021) - [j20]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): 1130-1141 (2021) - 2020
- [j19]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): 1249-1260 (2020) - [j18]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): D344-D353 (2020) - [j17]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): W132-W139 (2020)
2010 – 2019
- 2019
- [j16]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: baz047 (2019) - [j15]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): 4496-4498 (2019) - [j14]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): W345-W349 (2019) - 2018
- [j13]David Hoksza, Piotr Gawron, Marek Ostaszewski, Reinhard Schneider:
MolArt: a molecular structure annotation and visualization tool. Bioinform. 34(23): 4127-4128 (2018) - [j12]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): 39:1-39:12 (2018) - [c39]Radoslav Krivák, Lukás Jendele, David Hoksza:
Peptide-Binding Site Prediction From Protein Structure via points on the Solvent Accessible Surface. BCB 2018: 645-650 - [c38]Jan Jelínek, Petr Skoda, David Hoksza:
Software framework for similarity-based prediction of protein interfaces. BIBM 2018: 2759-2761 - 2017
- [j11]Richard Elias, David Hoksza:
TRAVeLer: a tool for template-based RNA secondary structure visualization. BMC Bioinform. 18(1): 487 (2017) - [j10]Jan Jelínek, Petr Skoda, David Hoksza:
Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites. BMC Bioinform. 18(15): 63-72 (2017) - [c37]Rastislav Galvanek, David Hoksza:
Template-based prediction of RNA tertiary structure using its predicted secondary structure. BIBM 2017: 2238-2240 - [c36]Petr Skoda, David Hoksza, Jan Jelínek:
Platform for ligand-based virtual screening integration. BIBM 2017: 2256-2259 - [c35]Radoslav Krivák, David Hoksza, Petr Skoda:
Improving quality of ligand-binding site prediction with Bayesian optimization. BIBM 2017: 2278-2279 - 2016
- [j9]Jakub Velkoborsky, David Hoksza:
Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization. J. Cheminformatics 8(1): 74:1-74:14 (2016) - [c34]Petr Skoda, David Hoksza:
Benchmarking platform for ligand-based virtual screening. BIBM 2016: 1220-1227 - [c33]Rastislav Galvanek, David Hoksza, Josef Pánek:
Template-based prediction of RNA tertiary structure. BIBM 2016: 1897-1900 - [c32]David Hoksza, Petr Skoda:
Using Bayesian modeling on molecular fragments features for virtual screening. CIBCB 2016: 1-6 - [c31]Jan Jelínek, Petr Skoda, David Hoksza:
Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites. ICCABS 2016: 1 - 2015
- [j8]Petr Cech, David Hoksza, Daniel Svozil:
MultiSETTER: web server for multiple RNA structure comparison. BMC Bioinform. 16: 253:1-253:8 (2015) - [j7]Radoslav Krivák, David Hoksza:
Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features. J. Cheminformatics 7: 12 (2015) - [j6]David Hoksza, Daniel Svozil:
Multiple 3D RNA Structure Superposition Using Neighbor Joining. IEEE ACM Trans. Comput. Biol. Bioinform. 12(3): 520-530 (2015) - [c30]Radoslav Krivák, David Hoksza:
P2RANK: Knowledge-Based Ligand Binding Site Prediction Using Aggregated Local Features. AlCoB 2015: 41-52 - [c29]Petr Skoda, David Hoksza:
Exploration of topological torsion fingerprints. BIBM 2015: 822-828 - [c28]Martin Sícho, Daniel Svozil, David Hoksza:
Activity-driven exploration of chemical space with morphing. BIBM 2015: 1024-1031 - [c27]David Hoksza, Jan Jelínek:
Using Neo4j for Mining Protein Graphs: A Case Study. DEXA Workshops 2015: 230-234 - 2014
- [j5]David Hoksza, Petr Skoda, Milan Vorsilák, Daniel Svozil:
Molpher: a software framework for systematic chemical space exploration. J. Cheminformatics 6(1): 7 (2014) - [c26]David Hoksza, Petr Skoda:
Scaffold-based chemical space exploration. BIBM 2014: 1-3 - [c25]Josef Pánek, Jan Hajic, David Hoksza:
Template-based prediction of ribosomal RNA secondary structure. BIBM 2014: 18-20 - [c24]David Hoksza, Petr Skoda:
2D Pharmacophore Query Generation. ISBRA 2014: 289-300 - 2013
- [j4]Jirí 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) - [c23]Petr Skoda, David Hoksza:
Chemical space visualization using ViFrame. ICIS 2013: 541-546 - [c22]Jirí Novák, Timo Sachsenberg, David Hoksza, Tomás Skopal, Oliver Kohlbacher:
A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools. PACBB 2013: 101-109 - [c21]David Hoksza, Peter Szépe, Daniel Svozil:
MultiSETTER - Multiple RNA Structure Similarity Algorithm. BSB 2013: 59-70 - 2012
- [j3]David Hoksza, Daniel Svozil:
Efficient RNA pairwise structure comparison by SETTER method. Bioinform. 28(14): 1858-1864 (2012) - [j2]Jirí Novák, Tomás Skopal, David Hoksza, Jakub Lokoc:
Non-metric similarity search of tandem mass spectra including posttranslational modifications. J. Discrete Algorithms 13: 19-31 (2012) - [j1]Petr Cech, Daniel Svozil, David Hoksza:
SETTER: web server for RNA structure comparison. Nucleic Acids Res. 40(Web-Server-Issue): 42-48 (2012) - [c20]Jakub Galgonek, Tomás Skopal, David Hoksza:
P3S: Protein Structure Similarity Search. Euro-Par Workshops 2012: 228-237 - [c19]Jakub Galgonek, Martin Krulis, David Hoksza:
On the Parallelization of the SProt Measure and the TM-Score Algorithm. Euro-Par Workshops 2012: 238-247 - [c18]Jirí Novák, David Hoksza, Jakub Lokoc, Tomás Skopal:
On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering. ISBRA 2012: 189-200 - [c17]Jirí Novák, Jakub Galgonek, David Hoksza, Tomás Skopal:
SimTandem: Similarity Search in Tandem Mass Spectra. SISAP 2012: 242-243 - 2011
- [c16]David Hoksza, Daniel Svozil:
Exploration of Chemical Space by Molecular Morphing. BIBE 2011: 201-208 - [c15]David Hoksza, Daniel Svozil:
SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm. ISBRA 2011: 37-48 - [c14]Jakub Galgonek, David Hoksza:
On metric approximations of the SProt measure. SISAP 2011: 119-120 - [c13]Jirí Novák, Tomás Skopal, David Hoksza, Jakub Lokoc, Jakub Galgonek:
Protein sequences identification using NM-tree. SISAP 2011: 125-126 - 2010
- [c12]Jakub Galgonek, David Hoksza:
SProt - from local to global protein structure similarity. BIBM Workshops 2010: 124-129 - [c11]Jirí Novák, David Hoksza:
Similarity search and posttranslational modifications in tandem mass spectra. BIBM Workshops 2010: 845-846 - [c10]Jirí Novák, David Hoksza:
Parametrised Hausdorff Distance as a Non-Metric Similarity Model for Tandem Mass Spectrometry. DATESO 2010: 1-12 - [c9]Jirí Novák, Tomás Skopal, David Hoksza, Jakub Lokoc:
Improving the similarity search of tandem mass spectra using metric access methods. SISAP 2010: 85-92
2000 – 2009
- 2009
- [c8]Jirí Novák, David Hoksza:
An application of the metric access methods to the mass spectrometry data. CIBCB 2009: 220-227 - [c7]David Hoksza:
DDPIn - Distance and density based protein indexing. CIBCB 2009: 263-270 - [c6]Jakub Galgonek, David Hoksza:
On the Effectiveness of Distances Measuring Protein Structure Similarity. SISAP 2009: 165-166 - 2008
- [c5]David Hoksza, Tomás Skopal:
Native Multidimensional Indexing in Relational Databases. COMAD 2008: 251-260 - [c4]David Hoksza:
Improved Alignment of Protein Sequences Based on Common Parts. ISBRA 2008: 87-99 - 2007
- [c3]Tomás Skopal, David Hoksza:
Improving the Performance of M-Tree Family by Nearest-Neighbor Graphs. ADBIS 2007: 172-188 - [c2]Tomás Skopal, David Hoksza, Jaroslav Pokorný:
Construction of Tree-Based Indexes for Level-Contiguous Buffering Support. DASFAA 2007: 361-373 - [c1]David Hoksza, Tomás Skopal:
Index-Based Approach to Similarity Search in Protein and Nucleotide Databases. DATESO 2007
Coauthor Index
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