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Course, academic year 2022/2023
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Molecular dynamics - calculations of free energy - NBCM181
Title: Molekulární dynamika - výpočty volné energie
Guaranteed by: Institute of Physics of Charles University (32-FUUK)
Faculty: Faculty of Mathematics and Physics
Actual: from 2020
Semester: both
E-Credits: 3
Hours per week, examination: 1/2, MC [HT]
Capacity: unlimited
Min. number of students: unlimited
Virtual mobility / capacity: no
State of the course: taught
Language: Czech
Teaching methods: full-time
Teaching methods: full-time
Note: you can enroll for the course in winter and in summer semester
Guarantor: RNDr. Ivan Barvík, Ph.D.
RNDr. Ondřej Maršálek, Ph.D.
Annotation -
Last update: prof. RNDr. Marek Procházka, Ph.D. (28.01.2019)
Protein-ligand binding and drug partitioning across the cell membrane, which are of paramount importance in the field of computer-aided, rational drug design, cannot be predicted reliably without the knowledge of the associated free energy changes. These lessons and practical exercises provide a systematic review of the methods that can be used for free energy calculations.
Course completion requirements - Czech
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.

Literature - Czech
Last update: prof. RNDr. Marek Procházka, Ph.D. (28.01.2019)

Ch. Chipot, A. Pohorille

Free Energy Calculations - Theory and Applications in Chemistry and Biology

Syllabus -
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

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