| This series of lectures provides an introduction to the theoretical study of biomolecules, focusing on proteins and nucleic acids.
After a brief introduction to the basic principles of quantum chemistry, the following class lectures will focus on intermolecular interactions, structure and the dynamics of biomolecules. Exercises will provide insight into how to obtain the structure and properties of relative small molecules (tens of atoms) using ab initio methods as well as how to apply computer experiments from larger systems (hundreds or thousands)to biological interest. Students will become familiar using the UNIX operating system, molecular modeling and computer graphics.
1. Introduction to quantum theory: Schrödinger equation and its approximations, valence bond theory, wave function.
2. Computational methods of quantum and theoretical chemistry: ab initio approaches, semi-empirical methods, empirical force fields, molecular mechanics; commonly used programs in the computational chemistry.
3. Computational experiments and simulations: classical and ab initio molecular dynamics, Monte Carlo, calculations of statistical and thermodynamics values.
4. Intra- and intermolecular interactions in biomolecules.
5. Nucleic acids: structure and dynamics of nitrogenous bases and base pairs, simulations of large fragments (oligomers) of nucleic acids.
6. Proteins: structure and dynamics of amino acids, peptides, docking, combinatorial chemistry, QSAR methods.
7. UNIX operating system, basic commands, working with text editors.
8. Applications of the quantum chemical programs (GAUSSIAN, TURBOMOLE) , programs for empirical calculations (molecular mechanics and dynamic (AMBER, CHARMM).
9. Computer graphics: constructing a molecule, visualization of results obtained by computational experiments.
10. Structural databases in chemistry and biology: Retrieving of structures, statistical methods, data sorting and handling
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