| 1 |
Assessing the Performance of MM/PBSA, MM/GBSA, and QM-MM/GBSA Approaches on Protein/Carbohydrate Complexes: Effect of Implicit Solvent Models, QM Methods, and Entropic Contributions
Mishra SK, Koca J
Journal of Physical Chemistry B, 122(34), 8113, 2018 |
| 2 |
Exploring Reaction Pathways for O-GlcNAc Transferase Catalysis. A String Method Study
Kumari M, Kozmon S, Kuhanek P, Stepan J, Tvaroska I, Koca J
Journal of Physical Chemistry B, 119(12), 4371, 2015 |
| 3 |
Bioinformatics and Molecular Dynamics Simulation Study of L1 Stalk Non-Canonical rRNA Elements: Kink-Turns, Loops, and Tetraloops
Krepl M, Reblova K, Koca J, Sponer J
Journal of Physical Chemistry B, 117(18), 5540, 2013 |
| 4 |
Substrate-Assisted Catalytic Mechanism of O-GIcNAc Transferase Discovered by Quantum Mechanics/Molecular Mechanics Investigation
Tvaroska I, Kozmon S, Wimmerova M, Koca J
Journal of the American Chemical Society, 134(37), 15563, 2012 |
| 5 |
Mechanism of hydrogen-bond array isomerization in tetrahydroxycalix[4]arene and tetrahydroxythiacalix[4]arene
Matousek J, Cajan M, Kulhanek P, Koca J
Journal of Physical Chemistry A, 112(5), 1076, 2008 |
| 6 |
Electronegativity equalization method: Parameterization and validation for large sets of organic, organohalogene and organometal molecule
Varekova RS, Jirouskova Z, Vanek J, Suchomel S, Koca J
International Journal of Molecular Sciences, 8(7), 572, 2007 |
| 7 |
Effect of solvation on pinched cone-pinched cone interconversion of tetraethoxycalix[4]arene and tetraethoxythiacalix[4]arene
Matousek J, Kulhanek P, Cajan M, Koca J
Journal of Physical Chemistry A, 110(3), 861, 2006 |
| 8 |
Complexity and convergence of electrostatic and van der Waals energies within PME and cutoff methods
Varekova RS, Koca J, Zhan CG
International Journal of Molecular Sciences, 5(4-7), 154, 2004 |
| 9 |
Computer modeling and simulations on flexible bifunctional systems: Intramolecular energy transfer implications
Vrbka L, Klan P, Kriz Z, Koca J, Wagner PJ
Journal of Physical Chemistry A, 107(18), 3404, 2003 |
| 10 |
Mechanism of proton transfer in short protonated oligopeptides. 1. N-methylacetamide and N-2-acetyl-N-1-methylglycinamide
Kulhanek P, Schlag EW, Koca J
Journal of Physical Chemistry A, 107(30), 5789, 2003 |
