Teaching code

4S003658

Teacher

Alejandro Giorgetti

Coordinator

Alejandro Giorgetti

Credits

6

Language

English

Scientific Disciplinary Sector (SSD)

BIO/10 - BIOCHEMISTRY

Period

Semester 2 dal Mar 6, 2023 al Jun 16, 2023.

Lessons timetable Moodle Seminars 0

Learning objectives

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.

Prerequisites and basic notions

There are no prerequisites

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-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

Bibliography

Didactic methods

During the course different teaching techniques are used:
- Classical theoretical lessons
- Practical exercises on the PC (use of state-of-the-art programs for running molecular dynamics simulations, docking, and drug design)
- Literature analysis

Learning assessment procedures

Written.
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.

Evaluation criteria

The student must: -be able to master the specific language of modern computational biology. -be able to critically understand a scientific article in the field of computational biology -Know the theoretical basis of molecular dynamics and virtual docking

Criteria for the composition of the final grade

The final grade consists of: - Grade of the presentations to groups of high-impact scientific articles - Grade of the written exam during the exam session

Exam language

Inglese