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DBLP record for David Hoksza

journal paper, indexed by WoS, indexed by Scopus

2021 (1 publication)

  1. Blake A. Sweeney, David Hoksza, Eric P. Nawrocki, Carlos Eduardo Ribas, Fábio Madeira, Jamie J. Cannone, Robin Gutell, Aparna Maddala, Caeden D. Meade, Loren Dean Williams, Anton S. Petrov, Patricia P. Chan, Todd M. Lowe, Robert D. Finn, Anton I. Petrov. R2DT is a framework for predicting and visualising RNA secondary structure using templates, Nature communications, 12(3494 ), Nature, ISSN: 2041-1723, 2021

2020 (5 publications)

  1. David Hoksza, RNAcentral Consoritum. RNAcentral 2021: secondary structure integration, improved sequence search, and new member databases, Nucleic Acids Research, Oxford Journals, ISSN: 1362-4962, 2020

  2. Sumaiya Iqbal, David Hoksza, Eduardo Perez-Palma, Patrick May, Jakob Berg Jespersen, Shehab Sarar Ahmed, Zaara Tasnim Rifat, Henrike O. Heyne, M. Sohel Rahman, Je rey R. Cottrell, Florence F. Wagner, Mark J. Daly, Arthur J. Campbell and Dennis Lal. MISCAST: MIssense variant to protein StruCture Analysis web SuiTe, Nucleic Acids Research, 48(W1), pp.: W132–W139, Oxford Journals, ISSN: 1362-4962, 2020

  3. PDBe-KB consortium, David Hoksza, Radoslav Krivák, Petr Škoda. PDBe-KB: a community-driven resource for structural and functional annotations, Nucleic Acids Research, 48(D1), pp.: D344–D353, Oxford Journals, ISSN: 1362-4962, 2020

  4. Sumaiya Iqbal, Eduardo Pérez-Palma, Jakob Berg Jespersen, Patrick May, David Hoksza, Henrike O. Heyne, Shehab S. Ahmed, Zaara T. Rifat, M Sohel Rahman, Kasper Lage, Aarno Palotie, Jeffrey R. Cottrell, Florence F. Wagner, Mark J. Daly, Arthur J Campbell, Dennis Lal. Comprehensive characterization of amino acid positions in protein structures reveals molecular effect of missense variants, Proceedings of the National Academy of Sciences of the United States of America (PNAS), United States National Academy of Sciences, ISSN: 1091-6490, 2020

  5. Piotr Gawron, David Hoksza, Janet Pinero, Maria Pena Chilet, Marina Esteban Jose Luis Fernandez, Vincenza Colonna, Joaquin Dopazo, Laura I. Furlong, Marek Ostaszewski. Disease and pathway maps for Rare Diseases, BioHackathon series: BioHackathon EUROPE, 2019, Paris, France, biohackrxiv, 2020

2019 (5 publications)

  1. David Hoksza, Piotr Gawron, Marek Ostaszewski, Ewa Smula, Reinhard Schneider. MINERVA API and plugins: opening molecular network analysis and visualization to the community, Bioinformaics, Oxford Journals, ISSN: 1460-2059, 2019

  2. David Hoksza. Piotr Gawron, Marek Ostaszewski, Jan Hausenauer, Reinhard Schneider. Closing the gap between formats for storing layout information in systems biology, Briefings in Bioinformatics, Oxford Journals, ISSN: 1477-4054, 2019

  3. David Hoksza, Josef Pánek, Jan Jelínek. rPredictorDB: A predictive database of individual secondary structures of RNAs and their formatted plots, DATABASE, 2019, Oxford Journals, ISSN: 1758-0463, 2019

  4. Sune S. Nielsen, Marek Ostaszewski, Fintan McGee, David Hoksza, Simone Zorzan. Machine Learning to Support the Presentation of Complex Pathway Graphs, IEEE/ACM Transactions on Computational Biology and Bioinformatics, IEEE, ISSN: 15455963, 2019

  5. Lukáš Jendele, Radoslav Krivák, Petr Škoda, Marian Novotný, David Hoksza. PrankWeb: a web server for ligand binding site prediction and visualization, Nucleic Acids Research, Oxford Journals, ISSN: 1362-4962, 2019

2018 (4 publications)

  1. David Hoksza, Piotr Gawron, Marek Ostaszewski and Reinhard Schneider. MolArt: A molecular structure annotation and visualization tool, Bioinformatics, Oxford Journals, 2018

  2. Radoslav Krivák, David Hoksza. P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure, Journal of Cheminformatics, 10(39), Springer, ISSN: 1758-2946, 2018

  3. Jan Jelínek, Petr Škoda, David Hoksza. Software framework for similarity-based prediction of protein interfaces, BIBM, Madrid, Spain, IEEE, ISBN: 978-1-5386-5488-0, 2018

  4. Radoslav Krivak, Lukáš Jendele, David Hoksza. Peptide-Binding Site Prediction From Protein Structure via points on the Solvent Accessible Surface, Computational Structural Bioinformatics Workshop, ACM-BCB, ACM, 2018

2017 (6 publications)

  1. Jan Jelínek, Petr Škoda, David Hoksza. Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites, BMC Bioinformatics, 18(Suppl. 15), Springer Nature, ISSN: 1471-2105, 2017

  2. Richard Eliáš, David Hoksza. TRAVeLer: a tool for Template-based RnA secondary structure visualization, BMC Bioinformatics, 18(847), Springer Nature, ISSN: 1471-2105, 2017

  3. David Hoksza, Rastislav Galvánek. Template-based prediction of RNA tertiary structure using its predicted secondary structure, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp.: 2238-2240, IEEE, ISBN: 978-1-5090-3050-7, 2017

  4. Radoslav Krivák, David Hoksza. Improving quality of ligand-binding site prediction with bayesian optimization, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE, 2017

  5. Petr Škoda, David Hoksza. Platform for ligand-based virtual screening, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE, 2017

  6. Rastislav Galánek, David Hoksza. Template-based prediction of RNA tertiary structure using its predicted secondary structure, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE, 2017

2016 (7 publications)

  1. Jan Pešek, David Hoksza. Large RNA secondary structure conservation annotation using secondary structure-based MSA, International Journal of Bioscience, Biochemistry and Bioinformatics, 6(1), pp.: 18-25, International Academy Publishing, ISSN: 2010-3638, 2016

  2. Richard Eliáš, David Hoksza. RNA secondary structure visualization using tree edit distance, International Journal of Bioscience, Biochemistry and Bioinformatics, 6(1), pp.: 9-17, International Academy Publishing, ISSN: 2010-3638, 2016

  3. Jakub Velkoborsky, David Hoksza. Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization, Journal of Cheminformatics, 8(74), Springer, ISSN: 1758-2946, 2016

  4. David Hoksza, Petr Škoda. Using Bayesian Modeling on Molecular Fragments Features for Virtual Screening, IEEE International Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2016), Chiang Mai, Thailand, IEEE, ISBN: 978-1-4673-9472-7, 2016

  5. Petr Škoda, David Hoksza. Benchmarking Platform for Ligand-Based Virtual Screening, BIBM Workshop on Health Informatics and Data Science (HI-DS), Shenzhen, China, pp.: 1225-1232, IEEE, ISBN: 978-1-5090-1610-5, 2016

  6. Rastislav Galvánek, David Hoksza, Josef Pánek. Template-based prediction of RNA tertiary structure, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shenzhen, 1902-1905, IEEE, ISBN: 978-1-5090-1610-5, 2016

  7. Jan Jelínek, Petr Škoda, David Hoksza. Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites, IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Atlanta, GA, USA, IEEE, ISBN: 978-1-5090-4199-2, 2016

2015 (6 publications)

  1. Petr Čech, David Hoksza, Daniel Svozil. MultiSETTER: web server for multiple RNA structure comparison, BMC Bioinformatics, 16(253), BioMed Central, ISSN: 1471-2105, 2015

  2. Radoslav Krivák, David Hoksza. Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features, Journal of Cheminformatics, 7(1), Chemistry Central, ISSN: 1758-2946, 2015

  3. Radoslav Krivák, David Hoksza. P2RANK: knowledge-based ligand binding site prediction using aggregated local features, AlCoB, Mexico City, Mexico, pp.: 41-52, Springer, ISBN: 978-3-319-21232-6, 2015

  4. Petr Škoda, David Hoksza. Exploration of Topological Torsion Fingerprints, BIBM Workshop on Health Informatics and Data Science (HI-DS), Washington, USA, IEEE, 2015

  5. Martin Šícho, Daniel Svozil, David Hoksza. Activity-Driven Exploration of Chemical Space with Morphing, International Workshop on Biomedical and Health Informatics, IEEE, 2015

  6. David Hoksza, Jan Jelínek. Using Neo4j for mining protein graphs: a case study, NoSQL-Net - International Workshop on NoSQL Databases, Emerging Database Technologies and Applications, DEXA, Valencia, Spain, pp.: 230-235, IEEE, ISBN: 978-1-4799-5722-4, 2015

2014 (6 publications)

  1. David Hoksza, Daniel Svozil. Multiple 3D RNA Structure Superposition Using Neighbor Joining, IEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics, PP(99), IEEE, ISSN: 1545-5963, 2014

  2. David Hoksza, Petr Škoda, Milan Voršilák and Daniel Svozil. Molpher: a software framework for systematic chemical space exploration, Journal of Cheminformatics, 6(7), Chemistry Central, ISSN: 1758-2946, 2014

  3. Petr Škoda, David Hoksza. Target-Oriented Generic Fingerprint-Based Molecular Representation, CSEIT, Computer Science & Information Technology (CS & IT), ISSN: 2231-5403, 2014

  4. David Hoksza, Petr Škoda. Scaffold-based chemical space exploration, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp.: 1-3, IEEE, 2014

  5. Josef Pánek, Jan Hajič jr., David Hoksza. Template-Based Prediction of Ribosomal RNA Secondary Structure, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Belfast, UK, pp.: 18-20, IEEE, 2014

  6. David Hoksza, Petr Škoda. 2D Pharmacophore Query Generation, ISBRA, Central South University, Zhangjiajie, China, Springer, 2014

2013 (6 publications)

  1. J. Novák, T. Sachsenberg, D. Hoksza, T. Skopal, O. Kohlbacher. On Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, Efficiency of Precursor Mass Filter and Dealing with Variable Modifications, Journal of Integrative Bioinformatics, 10(3), 2013

  2. J. Galgonek, M. Kruliš, D. Hoksza. On the Parallelization of the SProt Measure and the TM-score Algorithm, 3rd International Workshop on High Performance Bioinformatics and Biomedicine (HiBB), Rhodes Island, Greece, 7640, pp.: 238-247, Lecture Notes in Computer Science, Springer, ISSN: 0302-9743, 2013

  3. J. Galgonek, T. Skopal, D. Hoksza. P3S: Protein Structure Similarity Search, 3rd International Workshop on High Performance Bioinformatics and Biomedicine (HiBB), Rhodes Island, Greece, 7640, pp.: 228-237, Lecture Notes in Computer Science, Springer, ISSN: 0302-9743, 2013

  4. J. Novák, T. Sachsenberg, D. Hoksza, T. Skopal, O. Kohlbacher. A Statistical Comparison of SimTandem with State-of-the-Art Peptide Identification Tools, 7th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB), Salamanca, Spain, Advances in Intelligent and Soft-Computing (AISC), vol. 222, pp.: 101-109, Springer, 2013

  5. D. Hoksza, P. Szepe, D. Svozil. MultiSETTER - Multiple RNA Structure Similarity Algorithm, BSB (Brazilian Symposium on Bioinformatics), Recife, Brazil, pp.: 59-70, Springer, ISBN: 978-3-319-02623-7, 2013

  6. P. Škoda, D. Hoksza. Chemical Space Visualization Using ViFrame, International Conference on Computer and Information Science (ICIS 2013), Toki Messe, Niigata, Japan, pp.: 541 - 546, IEEE, ISBN: 978-147990174-6, 2013

2012 (5 publications)

  1. David Hoksza, Daniel Svozil. Efficient RNA pairwise structure comparison by SETTER method, Bioinformatics, 28(14), pp.: 1858 - 1864, Oxford Journals, ISSN: 1460-2059, 1367-4803, 2012

  2. J. Novák, T. Skopal, D. Hoksza, J. Lokoč. Non-metric Similarity Search of Tandem Mass Spectra Including Posttranslational Modifications, Journal of Discrete Algorithms, 13, pp.: 19-31, Elsevier, ISSN: 1570-8667, 2012

  3. P. Čech, D. Svozil, D. Hoksza. SETTER Web Server - the Web Server for RNA Structure Comparison, Nucleid Acids Research, 40(W1), pp.: W42-W48, Oxford Journals, ISSN: 1362-4962, 1460-2059, 2012

  4. J. Novák, D. Hoksza, J. Lokoč, T. Skopal. On Optimizing the Non-metric Similarity Search in Tandem Mass Spectra by Clustering, ISBRA, Dallas, TX, USA, LNBI 7292, pp.: 189-200, Springer, 2012

  5. J. Novák, J. Galgonek, D. Hoksza, T. Skopal. SimTandem: Similarity Search in Tandem Mass Spectra, SISAP, Toronto, Ontario, Canada, LNCS 7404, pp.: 242-243, Springer, 2012

2011 (5 publications)

  1. J. Galgonek, D. Hoksza, T. Skopal. SProt: sphere-based protein structure similarity algorithm, Proteome Science, 9(Supplment 1), pp.: S20, BioMed Central, ISSN: 1477-5956, 2011,
    application/pdf iconFull article

  2. D. Hoksza, D. Svozil. Exploration of Chemical Space by Molecular Morphing, BIBE, Taichung, Taiwan, pp.: 201-208, IEEE, ISBN: 978-3-642-21259-8, 2011

  3. D. Hoksza, D.Svozil. SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm, ISBRA, Changsha, China, pp.: 37-49, LNBI, Springer Verlag, ISBN: 978-0-7695-4391-8, ISSN: 0302-9743, 2011,
    application/pdf iconFull article
    application/pdf iconPresentation

  4. J. Novák, T. Skopal, D. Hoksza, J. Lokoč, J. Galgonek. Protein Sequences Identification using NM-tree, SISAP, Lipari, Italy, pp.: 125-126, ACM, ISBN: 978-1-4503-0795-6, 2011

  5. J. Galgonek, D. Hoksza. On Metric Approximations of the SProt Measure, SISAP 2011: Fourth International Conference on Similarity Search and Applications, Lipari, Italy, pp.: 119-120, ACM, ISBN: 978-1-4503-0795-6, 2011

2010 (6 publications)

  1. D. Hoksza, J. Galgonek. Alignment-Based Extension to DDPIn Feature Extraction, International Journal of Computational Bioscience, (1), pp.: 79-87, Acta Press, ISSN: 1918-3909, 2010

  2. D. Hoksza. Similarity Search in Protein Databases, 2010

  3. J. Novák, D. Hoksza. Similarity Search and Posttranslational Modifications in Tandem Mass Spectra, BIBM, Hong Kong, China, pp.: 845-846, IEEE, ISBN: 978-1-4244-8302-0, 2010

  4. J. Galgonek, D. Hoksza. SProt - From Local to Global Protein Structure Similarity, BIBM'10 International Workshop on Computational Proteomics, Hong Kong, China, pp.: 124-129, IEEE, ISBN: 978-1-4244-8302-0, 2010

  5. J. Novák, D. Hoksza. Parametrised Hausdorff Distance as a Non-Metric Similarity Model for Tandem Mass Spectrometry, DATESO, Štědronín - Plazy, Czech Republic, pp.: 1-12, CEUR proceedings, ISSN: 1613-0073, 2010

  6. J. Novák, T. Skopal, D. Hoksza, J. Lokoč. Improving the Similarity Search of Tandem Mass Spectra using Metric Access Methods, SISAP, Istanbul, Turkey, pp.: 85-92, ACM, ISBN: 978-1-4503-0420-7, 2010

2009 (4 publications)

  1. J. Novák, D. Hoksza. An Application of the Metric Access Methods to the Mass Spectrometry Data, CIBCB, Nashville, TN, USA, pp.: 220-227, IEEE, ISBN: 978-1-4244-2756-7, 2009

  2. D. Hoksza, J. Galgonek. Density-Based Classification of Protein Structures Using Iterative TM-score, CSBW 2009 (workshop at BIBM 2009), Wahsington, D.C., USA, pp.: 87-93, IEEE, ISBN: 978-1-4244-5121-0, 2009

  3. D. Hoksza. DDPIn - Distance and Density Based Protein Indexing, IEEE CIBCB, Nashville, TN, USA, pp.: 263-270, IEEE, ISBN: 978-1-4244-2783-3, 2009

  4. J. Galgonek, D. Hoksza. On the Effectiveness of Distances Measuring Protein Structure Similarity, SISAP 2009: Second international workshop on similarity search and applications, Prague, Czech Republic, pp.: 165-166, IEEE, ISBN: 978-0-7695-3765-8, 2009

2008 (3 publications)

  1. D. Hoksza, T. Skopal. Native Multidimensional Indexing in Relational Databases, COMAD, Mumbai, India, pp.: 251-261, Computer Society of India, 2008

  2. D. Hoksza. Methods of Protein Structure Alignment, DATAKON, Brno, Czech Republic, ISBN: 978-80-7355-081-3, 2008

  3. D. Hoksza. Improved Alignment of Protein Sequences Based on Common Parts, ISBRA, Atlanta, GA, USA, pp.: 87-99, LNBI, Springer Verlag, ISSN: 0302-9743, 2008

2007 (4 publications)

  1. T. Skopal, D. Hoksza. Improving the Performance of M-tree Family by Nearest-Neighbor Graphs, ADBIS, Varna, Bulgaria, LNCS 4690, Springer, 2007

  2. T. Skopal, D. Hoksza, J. Pokorný. Construction of Tree-based Indexes for Level-Contiguous Buffering Support, DASFAA, Bangkok, Thailand, LNCS 4443, Springer, 2007

  3. D. Hoksza, T. Skopal. Index-based approach to similarity search in protein and nucleotide databases, DATESO, Desná-Èerná Øíèka, Czech Republic, CEUR proceedings, ISSN: 1613-0073, 2007

  4. D. Hoksza. Metric indexing of protein databases and promising approaches, WDS, Prague, Czech Republic, pp.: 91-98, Matfyzpress, 2007

2006 (1 publication)

  1. David Hoksza. Multidimensional indexing for relation databases, 2006



by Dr. Radut.