Description of the various biomolecular classes.
Intra- and intermolecular interactions. The role of water.
The 20 naturally occurring amino acids and their physicochemical properties. Protein primary, secondary and tertiary structure.
Protein thermodynamics and folding. Importance of heteropolymeric character for the stabilization of a unique native structure. Application of the Random Energy Model in protein stability. The helix-coil transition.
Examples of protein action.
Hemoglobin and models of allostery.
Basic elements of biomolecular modeling. Typical energy functions used in biomolecular modeling.
Normal mode calculations and their application in the study of protein properties.
Biomolecular dynamics simulations.
Implicit solvent models. Continuum electrostatic approximations (Poisson-Boltzmann and Generalized Born).
MD-based Free-energy calculations (method of thermodynamics integration and thermodynamic perturbation). Application of implicit-solvent and MD-based free-energy methods in the study of biomolecular association).