1. Physics of Protein Folding

2. Why is the protein folding problem important? Understanding the function Drug design Types of experiments: X-ray crystallography NMR Computer simulation

3. SMMP (Simple Molecular Mechanics for Proteins) Definition of internal coordinates

4. SMMP Definition of dihedral angles The bond 1-4 is rotated around the axis 2-3 by the angle φ until coinciding with the shaded plane

5. Energy

6. SMMP Input files The sequence filesequence The configuration file {residue(s) : variable(s) : value}configuration The library filelibrary file

7. SMMP

8. Simulations Minimization of protein conformations Simulated annealing Monte Carlo simulation in generalized ensembles

9. Structure prediction PDB file format: Start.pdbStart.pdb (Before running the package) Final.pdb Final.pdb (Result)

10. Visual Interpretation