prof. RNDr. Michal Otyepka, Ph.D.

2015

• Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields

  HAVRILA Marek ZGARBOVÁ Marie JUREČKA Petr BANÁŠ Pavel KREPL Miroslav OTYEPKA Michal ŠPONER Jiří

  Article in Periodical

  Journal of Physical Chemistry B, year: 2015, volume: 119, edition: 49, DOI

• MOLE 2.5: Improved Tool for Analysis of Ligand-Accessible Channels

  PRAVDA Lukáš BERKA Karel SVOBODOVÁ VAŘEKOVÁ Radka SEHNAL David OTYEPKA Michal KOČA Jaroslav

  Appeared in Conference without Proceedings

  Year: 2015, type: Appeared in Conference without Proceedings

• Molecular dynamic simulations of protein/RNA complexes: CRISPR/Csy4 endoribonuclease

  ESTARELLAS MARTIN Carolina OTYEPKA Michal KOČA Jaroslav BANÁŠ Pavel KREPL Miroslav ŠPONER Jiří

  Article in Periodical

  BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, year: 2015, volume: 1850, edition: 5, DOI

• Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with epsilon/zeta Force Field Reparametrizations

  MLÝNSKÝ Vojtěch KÜHROVÁ Petra ZGARBOVÁ Marie JUREČKA Petr WALTER Nils G. OTYEPKA Michal ŠPONER Jiří BANÁŠ Pavel

  Article in Periodical

  Journal of Physical Chemistry B, year: 2015, volume: 119, edition: 11, DOI

• Refinement of the Sugar-Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B-DNA

  ZGARBOVÁ M. ŠPONER Jiří OTYEPKA Michal CHEATHAM T.E. GALINDO-MURILLO R. JUREČKA P.

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2015, volume: 11, edition: 12, DOI

• Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics

  SRIPATHI Kamali N. BANÁŠ Pavel RÉBLOVÁ Kamila ŠPONER Jiří OTYEPKA Michal WALTER Nils G.

  Article in Periodical

  Physical Chemistry Chemical Physics, year: 2015, volume: 17, edition: 8, DOI

2014

• Anatomy of enzymatic channels and algorithm for its detection

  PRAVDA Lukáš SVOBODOVÁ VAŘEKOVÁ Radka SEHNAL David IONESCU Crina-Maria BERKA Karel OTYEPKA Michal KOČA Jaroslav

  Appeared in Conference without Proceedings

  Year: 2014, type: Appeared in Conference without Proceedings

• Anatomy of Enzyme Channels

  PRAVDA Lukáš BERKA Karel SVOBODOVÁ VAŘEKOVÁ Radka SEHNAL David BANÁŠ Pavel ROMAN A Laskowski KOČA Jaroslav OTYEPKA Michal

  Article in Periodical

  BMC Bioinformatics, year: 2014, volume: 15, edition: november, DOI

• Base Pair Fraying in Molecular Dynamics Simulations of DNA and RNA

  ZGARBOVÁ Marie OTYEPKA Michal ŠPONER Jiří LANKAŠ Filip JUREČKA Petr

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2014, volume: 10, edition: 8, DOI

• Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

  MLÝNSKÝ Vojtěch BANÁŠ Pavel ŠPONER Jiří VAN DER KAMP Marc W. MULHOLLAND Adrian J. OTYEPKA Michal

  Article in Periodical

  Journal of Chemical Theory and Computation, year: 2014, volume: 10, edition: 4, DOI