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. Molecular Mechanics
   • bonding and non-bonding terms
   • force-field parametrisation
   • parametrisation from ab-initio methods
4. Minimisation methods
   • First order methods
   • Second order methods
   • Choice of method
5. Molecular dynamics principles
   • The Verlet algorithm
   • Statistical ensembles
   • Monitoring equilibrium
   • Properties as statistical averages
6. Analysis of molecular dynamics trajectories
   • Evaluation of thermodynamic parameters
   • Structural indicators
   • Graphical visualization of a trajectory
7. First-principle molecular dynamics
   • Density-functional theory
   • Plane waves and pseudopotentials
   • Car-Parrinello molecular dynamics

Lectures

19/02 – 14.30-17.30
20/02 – 14.30-17.30
21/02 – 14.30-17.30

27/02 – 14.30-17.30
28/02 – 14.30-16.30