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Curriculum Vitae

Phone:   (+420) 951 554 406
Fax:       (+420) 221 914 323
E-mail:   hoksza (at) ksi (dot) mff (dot) cuni (dot) cz

Charles University in Prague, Czech Republic
Faculty of Mathematics and Physics, School of Computer Science 

  • Ph.D., Software Systems, September 2010
  • Thesis: Similarity Search in Protein Databases
  • Advisor: Tomáš Skopal, PhD.
  • RNDr., Software Systems, September 2008
  • M.Sc., Data Engineering, August 2006
  • Thesis: Multidimensional Indexing in Relational Databases
  • Advisor: Tomáš Skopal, PhD.


  • bioinformatics : structural bioinformatics, protein sequence and structure databases, rna sequence and structure databases
  • cheminformatics : chemical space exploration, virtual screening
  • databases : indexing, metric indexing, non-metric indexing

Assistant Professor (July 2012 - present)
Department of Software EngineeringSchool of Computer ScienceFMP,
Charles University in Prague

Researcher (September 2010 - June 2012)
Department of Software Engineering, School of Computer Science, FMP,
Charles University in Prague

Assistant Professor (September 2010 - February 2015)
Lecturer (September 2006 - August 2008)
Department of Computer Science and Mathematics, 



Georg-August-Universität Göttingen,
Institut für Informatik

January 2015

Knowledge-based modification of conditional random fields protein-protein identification method


Helmholtz Zentrum MunchenInstitute of Bioinformatics and Systems Biology
Chemoinformatics & Chemical Biology group

January 2012 – April 2012

Application of similarity search in protein active sites databases to the drug side effects prediciton


David Hoksza, Petr Škoda. 2D Pharmacophore Query Generation, ISBRA, Springer, , 2014
Martin Šícho, Daniel Svozil, David Hoksza. Activity-Driven Exploration of Chemical Space with Morphing, International Workshop on Biomedical and Health Informatics, IEEE, , 2015
D. Hoksza, J. Galgonek. Alignment-Based Extension to DDPIn Feature Extraction, International Journal of Computational Bioscience, Acta Press, (1), ISSN: 1918-3909, 2010
J. Novák, D. Hoksza. An Application of the Metric Access Methods to the Mass Spectrometry Data, CIBCB, IEEE, ISBN: 978-1-4244-2756-7, 2009
P. Škoda, D. Hoksza. Chemical Space Visualization Using ViFrame, International Conference on Computer and Information Science (ICIS 2013), IEEE, ISBN: 978-147990174-6, 2013
T. Skopal, D. Hoksza, J. Pokorný. Construction of Tree-based Indexes for Level-Contiguous Buffering Support, DASFAA, Springer, LNCS 4443 , 2007
D. Hoksza. DDPIn - Distance and Density Based Protein Indexing, IEEE CIBCB, IEEE, ISBN: 978-1-4244-2783-3, 2009
D. Hoksza, J. Galgonek. Density-Based Classification of Protein Structures Using Iterative TM-score, CSBW 2009 (workshop at BIBM 2009), IEEE, ISBN: 978-1-4244-5121-0, 2009
David Hoksza, Daniel Svozil. Efficient RNA pairwise structure comparison by SETTER method, Bioinformatics, Oxford Journals, 28(14), ISSN: 1460-2059, 1367-4803, 2012
D. Hoksza, D. Svozil. Exploration of Chemical Space by Molecular Morphing, BIBE, IEEE, ISBN: 978-3-642-21259-8, 2011
Petr Škoda, David Hoksza. Exploration of Topological Torsion Fingerprints, BIBM Workshop on Health Informatics and Data Science (HI-DS), IEEE, , 2015
D. Hoksza. Improved Alignment of Protein Sequences Based on Common Parts, ISBRA, LNBI, Springer Verlag, , ISSN: 0302-9743, 2008
Radoslav Krivák, David Hoksza. Improving protein-ligand binding site prediction accuracy by classification of inner pocket points using local features, Journal of Cheminformatics, Chemistry Central, 7(1), ISSN: 1758-2946, 2015
T. Skopal, D. Hoksza. Improving the Performance of M-tree Family by Nearest-Neighbor Graphs, ADBIS, Springer, LNCS 4690 , 2007
J. Novák, T. Skopal, D. Hoksza, J. Lokoč. Improving the Similarity Search of Tandem Mass Spectra using Metric Access Methods, SISAP, ACM, ISBN: 978-1-4503-0420-7, 2010
D. Hoksza, T. Skopal. Index-based approach to similarity search in protein and nucleotide databases, DATESO, CEUR proceedings, , ISSN: 1613-0073, 2007
D. Hoksza. Methods of Protein Structure Alignment, DATAKON, ISBN: 978-80-7355-081-3, 2008
David Hoksza, Petr Škoda, Milan Voršilák and Daniel Svozil. Molpher: a software framework for systematic chemical space exploration, Journal of Cheminformatics, Chemistry Central, 6(7), ISSN: 1758-2946, 2014
David Hoksza, Daniel Svozil. Multiple 3D RNA Structure Superposition Using Neighbor Joining, IEEE IEEE/ACM Transactions on Computational Biology and Bioinformatics, IEEE, PP(99), ISSN: 1545-5963, 2014
D. Hoksza, P. Szepe, D. Svozil. MultiSETTER - Multiple RNA Structure Similarity Algorithm, BSB (Brazilian Symposium on Bioinformatics), Springer, ISBN: 978-3-319-02623-7, 2013
D. Hoksza, T. Skopal. Native Multidimensional Indexing in Relational Databases, COMAD, Computer Society of India, , 2008
J. Novák, T. Skopal, D. Hoksza, J. Lokoč. Non-metric Similarity Search of Tandem Mass Spectra Including Posttranslational Modifications, Journal of Discrete Algorithms, Elsevier, 13 , ISSN: 1570-8667, 2012
J. Galgonek, D. Hoksza. On the Effectiveness of Distances Measuring Protein Structure Similarity, SISAP 2009: Second international workshop on similarity search and applications, IEEE, ISBN: 978-0-7695-3765-8, 2009
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), Lecture Notes in Computer Science, Springer, 7640 , ISSN: 0302-9743, 2013
Radoslav Krivák, David Hoksza. P2RANK: knowledge-based ligand binding site prediction using aggregated local features, AlCoB, Springer, ISBN: 978-3-319-21232-6, 2015
J. Galgonek, T. Skopal, D. Hoksza. P3S: Protein Structure Similarity Search, 3rd International Workshop on High Performance Bioinformatics and Biomedicine (HiBB), Lecture Notes in Computer Science, Springer, 7640 , ISSN: 0302-9743, 2013
J. Novák, T. Skopal, D. Hoksza, J. Lokoč, J. Galgonek. Protein Sequences Identification using NM-tree, SISAP, ACM, ISBN: 978-1-4503-0795-6, 2011
D. Hoksza, D.Svozil. SETTER - RNA SEcondary sTructure-based TERtiary Structure Similarity Algorithm, ISBRA, LNBI, Springer Verlag, ISBN: 978-0-7695-4391-8, ISSN: 0302-9743, 2011
P. Čech, D. Svozil, D. Hoksza. SETTER Web Server - the Web Server for RNA Structure Comparison, Nucleid Acids Research, Oxford Journals, 40(W1), ISSN: 1362-4962, 1460-2059, 2012
D. Hoksza. Similarity Search in Protein Databases, , , 2010
J. Novák, J. Galgonek, D. Hoksza, T. Skopal. SimTandem: Similarity Search in Tandem Mass Spectra, SISAP, Springer, LNCS 7404 , 2012
J. Galgonek, D. Hoksza. SProt - From Local to Global Protein Structure Similarity, BIBM'10 International Workshop on Computational Proteomics, IEEE, ISBN: 978-1-4244-8302-0, 2010
J. Galgonek, D. Hoksza, T. Skopal. SProt: sphere-based protein structure similarity algorithm, Proteome Science, BioMed Central, 9(Supplment 1), ISSN: 1477-5956, 2011
Petr Škoda, David Hoksza. Target-Oriented Generic Fingerprint-Based Molecular Representation, CSEIT, Computer Science & Information Technology (CS & IT), , ISSN: 2231-5403, 2014
Josef Pánek, Jan Hajič jr., David Hoksza. Template-Based Prediction of Ribosomal RNA Secondary Structure, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE, , 2014
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, IEEE, ISBN: 978-1-4799-5722-4, 2015
  • Founding member of SIRET Research Group
  • Member of CSBMB (Czech Society For Biochemistry and Molecular Biology)
  • Member of FOBIA (Czech Free & Open BioInformatic Association)
  • Member of CSCH (Czech Chemical Society)


  • Nucleic Acids Research
  • Journal of Chemical Information and Modeling
  • Journal of Cheminformatics
  • Journal of Computer Mathematics
  • Journal of Molecular Graphics and Modelling
  • Current Bioinformatics
  • DKE Journal
  • ADBIS 2011
  • SISAP 2008, 2009, 2010, 2012
  • DATESO 2008, 2012
  • PACBB 2014, 2015
  • ENBIK 2012, 2014 — National Bioinformatics Conference
  • CSPUG seminars 2011, 2012 — co-organizing seminars of the Czech and Slovak PostgreSQL Group
  • DATESO 2007

Charles University in Prague, Prague, Czech Republic
Teaching Asistant & Assistant Professor (September 2006 – present)

  • Administration of MS SQL Server
  • Data organization and Processing
  • Database Systems
  • Database Applications
Institute of Chemical Technology, Prague, Czech Republic
Teaching Asistant & Assistant Professor (September 2011 – February 2015)
  • Bioinformatics Algorithms
  • Database Systems
Czech Technical University in Prague, Prague, Czech Republic
Teaching Asistant (September 2009 – September 2011)
  • Database Systems
  • Retrieval of Multimedia Content on the Web
  • Searching Web and Multimedia Databases
Lecturer (September 2006 - August 2008)
  • Introduction to Unix


Bernard Bolzano Foundation in Computer science Award

Awarded for the paper Density-Based Classification of Protein Structures Using Iterative TM-score, 2010

Werner Von Siemens Excellence Award

Honorable mention for the PhD thesis Similarity Search in Protein Databases, 2010

Programming Languages:

  •  C, C++, C#, ASP.NET, Java, JavaScript, PHP, UNIX shell scripting, SQL
  •  Microsoft SQL Server (TSQL programming, administration), Oracle(PL/SQL programming, administration), PostgreSQL (PG/SQL programming), Firebird (SQL programming), MySQL (SQL programming)