Master's degree in Molecular and Medical Biotechnology

Master's degree in Molecular and Medical Biotechnology

Computational Biology (2018/2019)

Course code
Alejandro Giorgetti
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Language of instruction


Teaching is organised as follows:
Activity Credits Period Academic staff
Modulo 1 3 II semestre Alejandro Giorgetti
Modulo 2 3 II semestre Alejandro Giorgetti

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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 dynamis simulations.


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-prtoein 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

Assessment methods and criteria

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.

Reference books
Activity Author Title Publisher Year ISBN Note
Modulo 1 Stefano Pascarella e Alessandro Paiardini Bioinformatica Zanichelli 2011 9788808062192
Modulo 1 Frishman, D., Valencia, Alfonso Modern Genome Annotation Springer 2008
Modulo 2 Stefano Pascarella e Alessandro Paiardini Bioinformatica Zanichelli 2011 9788808062192


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