| 1 |
Toward Ab Initio Protein Folding: Inherent Secondary Structure Propensity of Short Peptides from the Bioinformatics and Quantum-Chemical Perspective
Culka M, Galgonek J, Vymetal J, Vondrasek J, Rulisek L
Journal of Physical Chemistry B, 123(6), 1215, 2019 |
| 2 |
Effect of TFE on the Helical Content of AK17 and HAL-1 Peptides: Theoretical Insights into the Mechanism of Helix Stabilization
Vymetal J, Bednarova L, Vondrasek J
Journal of Physical Chemistry B, 120(6), 1048, 2016 |
| 3 |
Parametrization of 2,2,2-Trifluoroethanol Based on the Generalized Amber Force Field Provides Realistic Agreement between Experimental and Calculated Properties of Pure Liquid as Well as Water-Mixed Solutions
Vymetal J, Vondrasek J
Journal of Physical Chemistry B, 118(35), 10390, 2014 |
| 4 |
Optimal Definition of Inter-Residual Contact in Globular Proteins Based on Pairwise Interaction Energy Calculations, Its Robustness, and Applications
Fackovec B, Vondrasek J
Journal of Physical Chemistry B, 116(42), 12651, 2012 |
| 5 |
The DF-LCCSD(T0) correction of the phi/psi force field dihedral parameters significantly influences the free energy profile of the alanine dipeptide
Vymetal J, Vondrasek J
Chemical Physics Letters, 503(4-6), 301, 2011 |
| 6 |
Like-Charge Guanidinium Pairing from Molecular Dynamics and Ab Initio Calculations
Vazdar M, Vymetal J, Heyda J, Vondrasek J, Jungwirth P
Journal of Physical Chemistry A, 115(41), 11193, 2011 |
| 7 |
Gyration- and Inertia-Tensor-Based Collective Coordinates for Metadynamics. Application on the Conformational Behavior of Polyalanine Peptides and Trp-Cage Foldinge
Vymetal J, Vondrasek J
Journal of Physical Chemistry A, 115(41), 11455, 2011 |
| 8 |
Urea and Guanidinium Induced Denaturation of a Trp-Cage Miniprotein
Heyda J, Kozisek M, Bednarova L, Thompson G, Konvalinka J, Vondrasek J, Jungwirth P
Journal of Physical Chemistry B, 115(28), 8910, 2011 |
| 9 |
Metadynamics As a Tool for Mapping the Conformational and Free-Energy Space of Peptides - The Alanine Dipeptide Case Study
Vymetal J, Vondrasek J
Journal of Physical Chemistry B, 114(16), 5632, 2010 |
| 10 |
Loss of Dispersion Energy Changes the Stability and Folding/Unfolding Equilibrium of the Trp-Cage Protein
Cerny J, Vondrasek J, Hobza P
Journal of Physical Chemistry B, 113(16), 5657, 2009 |
