Regionální centrum pokročilých technologií a materiálů > Pracovníci > RNDr. Karel Berka, Ph.D.

RNDr. Karel Berka, Ph.D.

Email: karel.berka@upol.cz  
Location:17. listopadu 12, 771 46 Olomouc, Czech Republic 
Phone: (+420) 58 563 4769
Fax: (+420) 585 634 761

 

Professional:
Born: 19. 6. 1982
2001 – 2006 –  Mgr. (M.Sc. equivalent) in Physical chemistry, Faculty of Science Charles University in Prague
2008 –  RNDr. in Physical Chemistry, Faculty of Science, Charles University in Prague
2009 - Ph.D. in Modelling of chemical properties of nano- and biomaterials, Faculty of Science, Charles University in Prague with collaboration of Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic. 

Employment:
2010 – recent: Junior Researcher, Regional Centre of Advanced Technologies and Materials, PalackyUniversityinOlomouc
2010 – recent: PostDoc Fellow, Department of Physical Chemistry, PalackyUniversityinOlomouc
2007 – 2010: PhD student, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
2003 – 2006: Technician, Institute of Physiology, Academy of Sciences of the Czech Republic
2002 – 2003: Technician, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic

Research Activities:
Protein stabilization and function, molecular dynamics of biomolecules and their complexes, membrane protein simulations, small molecule docking, drug penetration through membranes.

Teaching Activites:
SS 2009/2010, 2010/2011 – Chapters from Physical Chemistry (KFC/KFCH, 2 h/week, lecturer)
WS 2010/2011, 2011/2012 – Physical Chemistry 2 (KFC/FC2, 2 h/week, teaching assistant)
WS 2010/2011, SS 2010/2011 – Bioinformatics and Computational Biology (KFC/BIN, 2 h/week, lecturer)
SS 2010/2011 – Physical Chemistry 1 (KFC/FC1, 2 h/week, teaching assistant)
WS 2011/2012 – Structural bioinformatics (KFC/STBI, 2 h/week, lecturer)

High school students:
One of authors of Korespondenční Seminář Inspirovaný Chemickou Tematikou (KSICHT) – www.ksicht.natur.cuni.cz – free-time teaching activities of high-school students in chemismy since 2001.
One of authors of Chemistry olympiad (ChO) category B (2008) and category A (2012).

Awards:
Dean award, Olomouc (2010), 1x Second best poster award, Prostab, Exeter, UK (2007)

Membership in scientific societies:
Co-founding author of KSICHT – Correspondence Seminar Inspired by Chemical Thematic for chemistry college education. Coauthor of physical chemistry part of Chemistry Olympiad 2011. Control committee member of FOBIA – Free and Open Bioinformatic Association.

Foreign visits:

 

2010 (Sep)               Université de Limoges, Limoges, France, group of dr. P. Trouillas
2009 (Aug-Oct)      POSTECH, Pohang, South Korea, group of prof. Kwang S. Kim
2008 (Nov)              EBI-EMBL, Hinxton, UK, group of prof. J. Thornton
2005 (Jul-Sep)       LBPA at ENS Cachan, Paris, France, group of prof. A. Lewit - Bentley

Publications -:
13  peer-reviewed scientific articles, 12 with Impact Factor, 86 citations; 78 without self-citations (11/28/2011), H-index: 5
17 conference contributions, 8 oral contributions.

Grants – Projects:
5 Research Grants/Projects, 1 as a principal investigator
GACR – 3, Research Centers – 2
2012-2014: GACR P303/12/P019 – principal investigator, post-doc grant

Top Publications

2011

  1. Oncak M, Berka K, Slavicek* P: Novel Covalent Bond in Proteins: Calculations on Model Systems Question the Bond Stability. Chem. Phys. Chem., accepted, 2011 (IF10 ~ 3.3)
  2. Berka, K.; Hendrychova, T.; Anzenbacher, P.; Otyepka, M. Membrane Position of Ibuprofen Agrees with Suggested Access Path Entrance to Cytochrome P450 2C9 Active Site. J. Phys. Chem. A, accepted, 2011 (IF10 ~ 2.7)
  3. Berka, K; Otyepka, M. Insenstivity to Close Contacts and Inability to Predict Protein Foldability Out of Thermodynamic Control? J. Biomol Struct Dyn 28(4), 633-634, 2011 (IF10 ~ 5.0)
  4. Kolář, M.; Berka, K.; Jurečka, P.; Hobza, P. On the Reliability of the AMBER Force Field and its Empirical Dispersion Contribution for the Description of Noncovalent Complexes. ChemPhysChem, 11 (11), 2399-2408, 2010 (IF09 ~ 3.5)
  5. Berka, K.; Laskowski, R.; Hobza, P.; Vondrášek, J., Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins. J. Chem. Theory Comput. 6(7), 2191-2203, 2010 (IF09 ~ 4.8)
  6. Berka, K.; Laskowski, R.; Riley, K. E.; Hobza, P.; Vondrášek, J., Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures J. Chem. Theory Comput., 5(4), 982-992, 2009 (IF09 ~ 4.8)
  7. Berka, K.; Hobza, P.; Vondrášek, J., Analysis of Energy Stabilization inside the Hydrophobic Core of Rubredoxin, ChemPhysChem, 10 (3),  543 – 548, 2009 (IF09 ~ 3.5)
  8. Biedermannova, L., Riley, K. E., Berka, K., Hobza, P. and Vondrášek, J., Another role of proline: stabilization interactions in proteins and protein complexes concerning proline and tryptophane Phys. Chem. Chem. Phys., 10, 6350 – 6359, 2008 (IF08 ~ 4.1)
  9. Řezáč, J., Jurečka, P., Riley, K. E., Černý, J., Valdes, H., Pluháčková, K., Berka, K., Řezáč, T., Pitoňák, M., Vondrášek, J., Hobza, P., Quantum chemical benchmark energy and geometry database for molecular clusters and complex molecular systems (www.begdb.com): A users manual and examples, Collect. Czech. Chem. Commun, 73 (10), 1261-1270, 2008 (IF08 ~ 0.8)
  10. Řezáč, J., Berka, K., Horinek, D., Hobza, P. and Vondrášek, J., The Stabilization Energy of the Glu-Lys Salt Bridge in the Protein/Water Environment: Correlated Quantum Chemical ab initio, DFT and Empirical Potential Studies., Collect. Czech. Chem. Commun, 73, 921-936, 2008 (IF08 ~ 0.8)

Older

Mazna, P., Berka, K., Jelinkova, I., Balik, A., Svoboda, P., Obsilova, V., Obsil, T., and Teisinger, J., Ligand binding to the human MT2 melatonin receptor: The role of residues in transmembrane domains 3, 6, and 7. Biochem. Biophys. Res. Commun., 332, 726-734, 2005. (IF05 ~ 3.0)
Mazna, P., Obsilova, V., Jelinkova, I., Balik, A., Berka, K., Sovova, Z., Ettrich, R., Svoboda, P., Obsil, T.,  and Teisinger, J., Molecular modeling of human MT2 melatonin receptor: the role of Val204, Leu272 and Tyr298 in ligand binding, J. Neurochem. 91, 836-842, 2004. (IF04 ~ 4.8)
Berka, K., Mazna, P., Jelínková, I., Balík, A., Svoboda, P., Obšilová, V., Obšil, T., and Teisinger, J., Molecular determinants of the agonist binding site of human MT2 melatonin receptor, Materials Structure, 12, 26, 2005

 

 


 

Ukázat publikace

Publikace

2012

  • [DOI] K. Berka, E. Anzenbacherova, T. Hendrychova, R. Lange, V. Masek, P. Anzenbacher, and M. Otyepka, “Binding of quinidine radically increases the stability and decreases the flexibility of the cytochrome P450 2D6 active site,” JOURNAL OF INORGANIC BIOCHEMISTRY, vol. 110, pp. 46-50, 2012.
  • [DOI] M. Paloncyova, K. Berka, and M. Otyepka, “Convergence of Free Energy Profile of Coumarin in Lipid Bilayer,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 8, iss. 4, pp. 1200-1211, 2012.
  • [DOI] P. Kosinova, K. Berka, M. Wykes, M. Otyepka, and P. Trouillas, “Positioning of Antioxidant Quercetin and Its Metabolites in Lipid Bilayer Membranes: Implication for Their Lipid-Peroxidation Inhibition,” JOURNAL OF PHYSICAL CHEMISTRY B, vol. 116, iss. 4, pp. 1309-1318, 2012.
  • M. Otyepka, K. Berka, and P. Anzenbacher, “Is There a Relationship Between the Substrate Preferences and Structural Flexibility of Cytochromes P450?,” CURRENT DRUG METABOLISM, vol. 13, iss. 2, pp. 130-142, 2012.
  • T. Hendrychova, K. Berka, V. Navratilova, P. Anzenbacher, and M. Otyepka, “Dynamics and Hydration of the Active Sites of Mammalian Cytochromes P450 Probed by Molecular Dynamics Simulations,” CURRENT DRUG METABOLISM, vol. 13, iss. 2, pp. 177-189, 2012.

2011

  • [DOI] M. Oncak, K. Berka, and P. Slavicek, “Novel Covalent Bond in Proteins: Calculations on Model Systems Question the Bond Stability,” CHEMPHYSCHEM, vol. 12, iss. 17, pp. 3449-3457, 2011.
  • [DOI] K. Berka, T. Hendrychova, P. Anzenbacher, and M. Otyepka, “Membrane Position of Ibuprofen Agrees with Suggested Access Path Entrance to Cytochrome P450 2C9 Active Site,” JOURNAL OF PHYSICAL CHEMISTRY A, vol. 115, iss. 41, pp. 11248-11255, 2011.
  • K. Berka and M. Otyepka, “Insenstivity to Close Contacts and Inability to Predict Protein Foldability,” JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, vol. 28, iss. 4, pp. 633-634, 2011.

2010

  • [DOI] M. Kolar, K. Berka, P. Jurecka, and P. Hobza, “On the Reliability of the AMBER Force Field and its Empirical Dispersion Contribution for the Description of Noncovalent Complexes,” CHEMPHYSCHEM, vol. 11, iss. 11, pp. 2399-2408, 2010.
  • [DOI] K. Berka, R. A. Laskowski, P. Hobza, and J. Vondrasek, “Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins,” JOURNAL OF CHEMICAL THEORY AND COMPUTATION, vol. 6, iss. 7, pp. 2191-2203, 2010.

2009

  • [DOI] K. Berka, P. Hobza, and J. Vondrasek, “Analysis of Energy Stabilization inside the Hydrophobic Core of Rubredoxin,” CHEMPHYSCHEM, vol. 10, iss. 3, pp. 543-548, 2009.

2008

  • [DOI] J. Rezac, P. Jurecka, K. E. Riley, J. Cerny, H. Valdes, K. Pluhackova, K. Berka, T. Rezac, M. Pitonak, J. Vondrasek, and P. Hobza, “QUANTUM CHEMICAL BENCHMARK ENERGY AND GEOMETRY DATABASE FOR MOLECULAR CLUSTERS AND COMPLEX MOLECULAR SYSTEMS (www.begdb.com): A USERS MANUAL AND EXAMPLES,” COLLECTION OF CZECHOSLOVAK CHEMICAL COMMUNICATIONS, vol. 73, iss. 10, pp. 1261-1270, 2008.