Introduction to the macromolecular (protein and nucleic acid) structure and experimental methods for determination of their 3D structures. Database of the experimentally determined 3D structures of proteins, nucleic acids and their complexes, "Protein Data Bank" (PDB). Molecular modelling methods, basic theory and difference between empirical and quantum mechanical methods. Meaning of force fields and parameterizations. Potential energy surface calculations and computational study of macromolecular structure, dynamics and reactivity. Energy minimization, molecular dynamics, stochastic dynamics, Monte Carlo methods. Importance of solvent for the complex formation. Modelling of solvent. Problem of treating the electrostatic interactions. Thermodynamics of macromolecular systems, ensembles, micro canonical, canonical, isothermal-isobaric. Computer programs for macromolecular modelling. Advance methods of molecular dynamics (accelerated, steered, random force, coarse grained. Principal components analysis, clustering, calculations of Gibbs potential, and the system entropy and enthalpy. Overview of the hybrid quantum mechanical - empirical methods for the study of (protein) enzyme catalysed chemical reactions.
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