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The goal of this course is to teach atomistic-level computational methods useful for pharmaceutical science and drug development. Students will learn the principles and practical applications of atomistic simulations. The course teaches how to predict experimental properties and critically interpret the results of atomistic simulations.
Last update: Dršatová Dita, Mgr. (22.10.2024)
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Demonstrate knowledge of the principles and ability to perform atomistic simulations. Last update: Dršatová Dita, Mgr. (22.10.2024)
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Obligatory:
Recommended:
Last update: Dršatová Dita, Mgr. (22.10.2024)
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Molecular representations: molecular graph, conformations, SMILES Quantum mechanics: Schrödinger equation, Hartree-Fock method, ground state, potential energy surface, ab initio forces, geometry optimization Classical molecular dynamics: equation of motion, force field, Verlet algorithm, system preparation, periodic boundary conditions, solvation, thermostat, barostat, equilibration Molecular dynamics analysis: root-mean-square deviation (RMSD), hydrogen bond analysis, data dimension reduction, kinetic models, Markov model, binding affinity prediction Introduction to basic experiments, spectroscopic methods, and chemical equilibrium models suitable for studying interactions between host molecule and ligand (i.e., host-guest complexation models). Determination of the equilibrium binding constant of the formed complex, its thermodynamic interpretation, and temperature dependence Last update: Dršatová Dita, Mgr. (22.10.2024)
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