Mgr. Pavel Banáš, Ph.D.

Education

1999 – 04
M.Sc. Analytical chemistry, Palacký University, Olomouc
2000 – 05
M.Sc. Applied physics, Palacký University, Olomouc
2005 – 09
Ph.D. Physical chemistry, Palacký University, Olomouc

Employment

2006 – 09
Researcher, Institute of Organic Chemistry and Biochemistry (group of Dr. Rulíšek), Prague
2008
Researcher, Palacký University, Olomouc
2009
Researcher, Institute of Biophysics (group of prof. Šponer), Brno

Visits

2004
Laboratory of Biomolecular Structure and Dynamics (prof. J. Koča), Masaryk University, Brno
2006
Stay at SISSA/ISAS Trieste, Italy, group of prof. Paolo Carloni
2009
BMC Uppsala, Sweden, group of prof. Johan Aqvist

Research specialization

Classical and quantum molecular dynamics of biomolecules, quantum chemical and hybrid QM/MM calculations and their application. RNA catalysis, structure and function of non-coding RNAs. Software development (e.g., CAVER).

Cooperation

Prof. Jiří Šponer, Institute of Biophysics, CAS, Brno - RNA.

Publications

Researcher's ID

Publications on PubMed

  1. Banas P, Walter NG, Sponer J, Otyepka M; Protonation States of the Key Active Site Residues and Structural Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics, J. Phys. Chem. B 114(26) 2010
  2. Mlynsky V, Banas P, Hollas D, Reblova K, Walter NG, Sponer J, Otyepka M; Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H(+) Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme, J. Phys. Chem. B 114(19) 2010
  3. Sponer JE*, Vázquez-Mayagoitia A, Sumpter BG, Leszczynski J, Sponer J*, Otyepka M, Banas P, Fuentes-Cabrera M*; Theoretical Study on the Intermolecular Interactions of Potentially Primordial Base Pair Analogues. Chemistry Eur. J. 16(10), 3057-3065, 2010 (Wiley InterScience)
  4. Pavlova M, Klvana M, Prokop Z, Chaloupkova R, Banas P, Otyepka M, Wade RC, Tsuda M, Nagata Y, Damborsky* J; Redesigning dehalogenase access tunnels as a strategy for degrading an anthropogenic substrate. Nature Chem. Biol., 5(10), 727-33, 2009 (Nature Publishing Group)
  5. Banas P, Jurecka P, Walter NG, Sponer J, Otyepka* M; Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM. (Invited Review) Methods, 49(2), 202-216, 2009 (ScienceDirect), (pdf)
  6. Banas P, Rulisek L, Hanosova V, Svozil D, Walter N, Sponer J, Otyepka M; General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility J Phys Chem B, 112(35), 11177-11187, 2008 (Am. Chem. Soc.)
  7. Sklenovsky P, Banas P, Otyepka M; Two C-terminal Ankyrin Repeats Form the Minimal Stable Unit of the Ankyrin Repeat Protein p18INK4c. J. Mol. Model. 14(8), 747-59, 2008 (Springer)
  8. Otyepka M, Banas P, Magistrato A, Carloni P, Damborsky J; Second step of hydrolytic dehalogenation in haloalkane dehalogenase investigated by QM/MM methods. Proteins: Struct. Funct. Bioinf. 70(3), 707-717, 2008 (Wiley InterScience)
  9. Damborsky J., Petrek M., Banas P., Otyepka M. Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles Biotechnol. J. 2, 65-67 2007 (Wiley InterScience) (pdf)
  10. Banas P, Otyepka M, Jerabek P, Petrek M, Damborsky J; Mechanism of Enhanced Conversion of 1,2,3-Trichloropropane by Mutant Haloalkane Dehalogenase Revealed by Molecular Modeling. J. Comput-Aid. Mol. Des. 20(6), 375-383, 2006 (pdf)
  11. Petrek M, Otyepka M, Banas P, Kosinova P, Koca J, Damborsky J; CAVER: A new tool to explore routes from protein clefts, pockets and cavities, BMC Bioinformatics 7:316 2006 (pdf)
  12. Banas P, Rehacek J, Hradil Z.; Perturbative quantum-state estimation, Phys. Rev. A 74(1), 014101, 2006