Lecturer:
Sara Fortuna, Federico Fogolari, Paolo Giannozzi (University of Udine)

Board Contact:
Federico Fogolari

1. Introduction to molecular modelling

• two-dimensional and three-dimensional models
• available databases
• molecular graphics

2. Protein structures and homology modelling

• sequence alignment with BLAST
• template identification
• building a model

3. Protein/protein complexed: docking

• methods to explore conformational space
• scoring functions
• docking algorithms

4. Molecular Mechanics

• bonding and non-bonding terms
• force-field parametrisation
• parametrisation from ab-initio methods

5. Minimisation methods

• First order methods
• Second order methods
• Choice of method

6. Molecular dynamics principles

• The Verlet algorithm
• Statistical ensembles
• Monitoring equilibrium
• Properties as statistical averages

7. Analysis of molecular dynamics trajectories

• Evaluation of thermodynamic parameters
• Structural indicators
• Graphical visualization of a trajectory

8. First-principle molecular dynamics

• Density-functional theory
• Plane waves and pseudopotentials
• Car-Parrinello molecular dynamics