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Last update: prof. RNDr. Marek Procházka, Ph.D. (28.01.2019)
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Last update: RNDr. Ivan Barvík, Ph.D. (15.05.2020)
Podmínkou udělení zápočtu je aktivní účast alespoň na 70 % hodin.
V případě nesplnění je nutno vypracovat úlohy z látky, kde došlo k absencím.
Podmínkou udělení zápočtu je dále vypracování zadaného projektu. |
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Last update: prof. RNDr. Marek Procházka, Ph.D. (28.01.2019)
Ch. Chipot, A. Pohorille Free Energy Calculations - Theory and Applications in Chemistry and BiologySpringer |
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Last update: prof. RNDr. Marek Procházka, Ph.D. (14.05.2020)
1. Pioneers of free energy calculations (1935 Kirkwood, 1938 Landau, 1954 Zwanzig, 1963 Widom, 1967 McDonald & Singer, 1984 McCammon, 1985 Jorgensen)
2. Examples of the use of free energy calculations (solvation free energy, comparison of the binding abilities of inhibitors to the active site of the enzyme, the effect of point mutations of amino acids on ligand binding, energy barrier during drug passage through the cell membrane)
3. Methods based on histograms and probability distributions
4. Calculations of free energy differences through perturbation theory
5. Thermodynamic integration
6. Alchemical calculations of free energy, thermodynamic cycles
7. Calculations of relative binding free energy
8. Calculations of absolute binding free energy
9. Free energy profile calculations
10. Umbrella Sampling Methods, Blue Moon, Adaptive Biasing Force, Metadynamics
11. Non-equilibrium methods for calculating equilibrium free energy
12. Free energy calculations as a tool for rational drug design |