Computational Biology (2020/2021)

Course code
Name of lecturer
Alejandro Giorgetti
Alejandro Giorgetti
Number of ECTS credits allocated
Academic sector
Language of instruction
II semestre dal Mar 1, 2021 al Jun 11, 2021.

Lesson timetable

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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

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

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.