doc. RNDr. Radka Svobodová, Ph.D.

Curriculum Vitae

Personal Information

• doc. RNDr. Radka Svobodová, Ph.D. , born 8.4.1977, married, 1 daughter

Department

• Central European Institute of Technology &
  National Centre for Biomolecular Research, Faculty of Science
  Masaryk University
  Kamenice 5, Bohunice, 625 00 Brno

Employment - Position

• Associate Professor

Education

• 2017: Doc., Biomolecular chemistry, Faculty of Science, Masaryk University
  2007: Ph.D., Biomolecular chemistry, Faculty of Science, Masaryk University
  2006: RNDr., Physical chemistry, Faculty of Science, Masaryk University
  2003: Mgr., Informatics, Faculty of Informatics, Masaryk University (with honours)
  2000: Mgr., Biochemistry, Faculty of Science, Masaryk University (with honours)
  

Employment

• 01/2022 – now: Head of core facility, CEITEC, Masaryk University
  08/2021 – now: Group leader, NCBR, Masaryk University
  02/2017 – now: Associate professor, NCBR & CEITEC, Masaryk University
  08/2009 – 01/2017: Assistant professor, NCBR & CEITEC, Masaryk University
  08/2009 – 10/2011: Project leader and researcher (external), Siemens, ANF DATA spol. s r.o.
  06/2007 – 07/2009: Section leader and researcher, Siemens, ANF DATA spol. s r.o.
  10/2004 – 05/2007: Team leader and researcher, Siemens, ANF DATA spol. s r.o.
  07/2003 – now: Lecturer (external), Faculty of Informatics, Masaryk University
  08/2001 – 09/2004: Software developer, Siemens, ANF DATA spol. s r.o.

Teaching Activities

• Teaching (the most important subjects): C2130 Introduction to chemoinformatics and bioinformatics, C2136 Advanced chemoinformatics, C2142 Design of algorithms in life sciences, PV082 Computational chemistry, PV027 Optimization, C2180 Project management of research projects I, C2181 Project management of research projects II, C2145 Structural bioinformatics in praxis
  Master and bachelor thesis – successfully finished: 39 master thesis (37x supervisor, 2x consultant), 39 bachelor thesis (36x supervisor, 3x consultant), 7 of the thesis obtained the Price of the dean
  Doctoral thesis – successfully finished: 8 doctoral students (1x supervisor, 7x consultant), 3 of the students were winners of the PhD Talent Challenge
  

Research Activities

• Scientometry:
  Journal full text papers: 51; book: 1; citations (in WoS): 1,812; h-index (in WoS): 20
  Bioinformatics software tools and databases: 20
  Researcher ID: E-2867-2012
  Scopus ID: 16235290700
  
• Research interests:
  Structural bioinformatics: definition, detection, comparison, characterization and validation of biomolecular fragments; channels and pores in biomacromolecules.
  Chemoinformatics: approaches for calculation of partial atomic charges, quantitative structure-property relationship models.
  Software development:Development of life science software tools and databases, data repositories, metadata processing, data management plans

Research fellowships

• 2014-2019: Protein Data Bank in Europe (Dr. Velankar group), EMBL-EBI, Hinxton, England (2-4 week stays each year)
  2015: RCSB Protein Data Bank, Rutgers, The State University of New Jersey, New Jersey, USA (one week)
  2015: Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark (one year)
  2004-2010: Life science group, Siemens Programming and System Engineering, Siemens, Vienna, Austria (regular business trips)
  2008-2009: Research & Development department, Siemens Industrial Mobility and Traffic Systems, Siemens, Munich, Germany (regular business trips)
  09-10/2010: Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland and Conway Institute, University College of Dublin, Dublin, Ireland
  07-10/2004: Bioinformatics group, Royal College of Surgeons in Ireland, Dublin, Ireland

University Activities

• Membership in academic institutions: Doctoral Board (programme Biomolecular chemistry and bioinformatics)
  ELIXIR CZ Head of Node for Masaryk University
  Others: Presentations at PhD days, Night of researchers, etc.

Activities Outside University

• ELIXIR Tools platform in Czech Republic
  Member of the 3D-BioInfo community in ELIXIR
  Member of the wwPDB consortium and the PDBe-KB consortium
  

Major Publications

• SEHNAL, David, S. BITTRICH, M. DESHPANDE, Radka SVOBODOVÁ, K. BERKA, V. BAZGIER, S. VELANKAR, S.K. BURLEY, Jaroslav KOČA a A.S. ROSE. Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic acids research. Oxford: Oxford University Press, roč. 49, W1, s. "W431"-"W437", 7 s. ISSN 0305-1048. doi:10.1093/nar/gkab314. 2021. URL info
• HUTAŘOVÁ VAŘEKOVÁ, Ivana, Jan HUTAŘ, Adam MIDLIK, Vladimír HORSKÝ, Eva HLADKÁ, Radka SVOBODOVÁ a Karel BERKA. 2DProts: database of family-wide protein secondary structure diagrams. Bioinformatics. Oxford University Press, roč. 37, č. 23, s. 4599-4601. ISSN 1367-4803. doi:10.1093/bioinformatics/btab505. 2021. URL info
• RAČEK, Tomáš, Ondřej SCHINDLER, Dominik TOUŠEK, Vladimír HORSKÝ, Karel BERKA, Jaroslav KOČA a Radka SVOBODOVÁ. Atomic Charge Calculator II: web-based tool for the calculation of partial atomic charges. Nucleic acids research. Oxford: Oxford University Press, roč. 48, W1, s. "W591"-"W596", 6 s. ISSN 0305-1048. doi:10.1093/nar/gkaa367. 2020. domovská stránka výsledku info
• PRAVDA, Lukáš, David SEHNAL, Dominik TOUŠEK, Veronika NAVRÁTILOVÁ, Václav BAZGIER, Karel BERKA, Radka SVOBODOVÁ VAŘEKOVÁ, Jaroslav KOČA a Michal OTYEPKA. MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Research. Oxford: Oxford University Press, roč. 46, W1, s. "W368"-"W373", 6 s. ISSN 0305-1048. doi:10.1093/nar/gky309. 2018. info
• SEHNAL, David, Mandar DESHPANDE, Radka SVOBODOVÁ VAŘEKOVÁ, Saqib MIR, Karel BERKA, Adam MIDLIK, Lukáš PRAVDA, Sameer VELANKAR a Jaroslav KOČA. LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data. Nature Methods. London, United Kingdom: Nature Publishing Group, roč. 14, č. 12, s. 1121-1122. ISSN 1548-7091. doi:10.1038/nmeth.4499. 2017. URL info

2022/04/24