Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored Using Classical and Random Acceleration Molecular Dynamics Simulations

Martin Klvaňa, Martina Pavlová, Táňa Koudeláková, +9

Journal of Molecular Biology

Molecular KineticsBiochemistryNatural SciencesBiocatalysisProduct Release +5

Non-Watson−Crick Base Pairing in RNA. Quantum Chemical Analysis of the cis Watson−Crick/Sugar Edge Base Pair Family

Judit E. Šponer, Nad’a Špačková, Petr Kulhánek, +1

The Journal of Physical Chemistry A

EngineeringMolecular BiologyComputational ChemistryChemistryChemical Biology +17

Evaluating Boundary Dependent Errors in QM/MM Simulations

Iván Solt, Petr Kulhánek, István Simon, +4

The Journal of Physical Chemistry B

Numerical AnalysisEngineeringDirect Numerical SimulationQm Region SizeMolecular Biology +22

Conformations of Flanking Bases in HIV-1 RNA DIS Kissing Complexes Studied by Molecular Dynamics

Kamila Réblová, Eva Fadrná, Joanna Sarzyńska, +4

Biophysical Journal

Bambusuril as a One-Electron Donor for Photoinduced Electron Transfer to Methyl Viologen in Mixed Crystals

Tomas Fiala, Lucie Ludvíková, Dominik Heger, +8

Journal of the American Chemical Society

An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5′-UAA/5′-GAN Internal Loops Studied by Molecular Dynamics Methods

Kamila Réblová, Zora Střelcová, Petr Kulhánek, +5

Journal of Chemical Theory and Computation

The Energy Gap as a Universal Reaction Coordinate for the Simulation of Chemical Reactions

Letif Mones, Petr Kulhánek, István Simon, +2

The Journal of Physical Chemistry B

EngineeringMolecular BiologyComplex SystemsComputational ChemistryChemistry +18

An RNA Molecular Switch: Intrinsic Flexibility of 23S rRNA Helices 40 and 68 5'-UAA/5'-GAN Internal Loops Studied by Molecular Dynamics Methods.

Kamila Réblová, Zora Střelcová, Petr Kulhánek, +5

PubMed

EngineeringStructural BioinformaticsMolecular BiologyChemical BiologyX-ray Arrangement +14

Electron Density Shift in Imidazolium Derivatives upon Complexation with Cucurbit[6]uril

Viktor Kolman, Radek Marek, Zora Střelcová, +4

Chemistry - A European Journal

EngineeringTheoretical Inorganic ChemistryOrganic ChemistryElectron Density ShiftChemistry +14

Probing the Two-Metal Ion Mechanism in the Restriction Endonuclease BamHI

Letif Mones, Petr Kulhánek, Jan Florián, +2

Biochemistry

Bioorganic ChemistryMolecular BiologyMolecular GeneticsChemical BiologyEnzymatic Modification +16