Learning outcomes of the course unit
The course has a practical formulation, with several practical exercises in the lab, to provide the students with advanced techniques and methodologies in the field of computational biophysics, in particular for the determination, prediction and analysis of the structure and the dynamics of proteic systems.
Basic knowledge of the structure of biological macromolecules.
Course contents summary
Structure of proteins. Covalent and not-covalent interactions that are present in a molecular structure. Theoretical and experimental methods to determine the secondary and tertiary structure of proteins. Topology. Supersecondary structures. Ramachandran plot. Fold classification.
Search engines in biological databases.
Protein and nucleic acid sequence analysis: similarity and sequence alignment tools (pairwise and multiple). Patterns and conserved motifs recognition. Protein physico-chemical profiles. Secondary structure prediction from the primary sequence.
Analysis of structural and functional features of proteins and protein complexes by means of molecular graphics softwares and web servers.
Computational techniques for the study of proteins’ structure and dynamics:
Comparative modeling and fold recognition methods.
Molecular mechanics and force fields; energy minimization; molecular dynamics simulations.
Molecular recognition. Molecular interaction simulations: docking and drug design.
Practices in the lab during the course.
A.M. Lesk, "Introduzione alla Bioinformatica", McGraw-Hill Ed.
G. Valle, M. Helmer Citterich, M. Attimonelli, G. Pesole, "Introduzione alla Bioinformatica", Zanichelli Ed.
D.E. Krane, M.L. Raymer, "Fondamenti di Bioinformatica", Pearson Education Ed.
Notes on the lessons and review articles will be given.
Oral lessons and practice in the laboratory.
Assessment methods and criteria
Discussions on the reports of the practices and oral examination on the fundamental concepts of the studied techniques.
A report on each practical exercise performed in the lab will be required.