COMPUTATIONAL BIOPHYSICS LABORATORY
Learning outcomes of the course unit
The course has a practical formulation. The practical exercises in the lab will be performed personally by the students, to provide them 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 protein systems.
Course contents summary
Protein structure. Covalent and not-covalent interactions that are present in a biomolecular structure. Theoretical and experimental methods for determining secondary and tertiary protein structure. Topological representation. 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 protein 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 protein 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, "Introduction to protein science", Oxford Univeristy Press.
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 practices 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.