The teaching is organized as follows:

Learning outcomes

This course gives an introduction to molecular computational biology and to the rational design of proteins using computational techniques. The arguments of the course include: molecular dynamis simulation techniques and advanced protein bioinformatics concepts.
At the end of the course the student should be able to:
- Deep and critical understanding of a scientific article where computational techniques are used
- Introduce (in silico) mutants able to affect the protein structure and/or function
- Prepare and run molecular dynamics simulations.

Program

Part A – Bioinformatics

− Advanced Structural Bioinformatics
- Thermodynamic basis of the stability of folded biomolecular structure
− Molecular basis of human perception


Part B – Molecular Modeling

− Basic elements of molecular modeling
− Electrostatic modeling
− Energy minimization based on force fields
− Molecular dynamics: solution by using the open source NAMD and/or Gromacs codes
− Conformational analysis


Part C – Ligand-protein interactions


− Protein assembly (protein-protein complexes, protein-protein interactions in protein dimers, crystals): protein-protein docking algorithms and programs
− Ligand Protein interaction: docking algorithms and programs
− Projects: Drug and/or protein design

Bibliography

Examination Methods

The examination is divide in two parts: the first consists in the presentation (in groups) of a scientific article in which state of the arte techniques are used.
The second part is a written examination with open questions regarding the arguments of the course.