1.Protein and Nucleic Acids Architecture Primary, secondary, tertiary, and quaternary structures, dihedral angles and Ramachandran plots, "Catalog" of protein interactions
2. Protein Folding Driving forces of protein folding, energy landscapes, folding in the chaperones, protein misfolding and aggregation, relation between function and dynamics, comparison between protein and RNA folding.
3. Modeling Interactions in Proteins: Building a force field bonded and non-bonded interactions, long-range interactions, different force-fields, parametrization
4. Simplified models of biomolecular systems Physical coarse-grained models, lattice models, empirical potential
5. Foundations of Biomolecular Simulations Classical vs. quantum descriptions, assumptions in biomolecular simulations, from all-atom to simplified (coarse grained) models
6. Energy minimization
7. Molecular Dynamics Simulations Idea of MD , Structure of MD code, Numerical integrators, Simulating different ensembles, Langevin dynamics, MD program packages, setting and running MD simulations, solvent models, conformational sampling
8. Monte Carlo Simulations Basics of MC method, MC simulations of lattice protein models
9. Normal Mode Analysis: dynamics of the folded state
10. Analyzing MD simulations time series, multiple histogram methods, Principal Component Analysis
11. Special topics strategies to enhance conformational sampling, steered MD