Learning outcomes of the course unit
To provide the students with the basic concepts and tools of the structural bioinformatics, from the sequence analysis, to the protein modelling and the computer simulations of molecular dynamics and interactions.
Basic knowledge of macromolecular structures.
Course contents summary
Sequence analysis : databases search for sequence and structures of nucleic acids and proteins; protein sequence identification from DNA fragments; automatic sequence comparation by means of softwares based on the recognition of high local similarity regions; recognition and analysis of characteristic patterns in the sequences; pairwise and multiple sequence alignments; protein secondary structure prediction from the primary sequence; protein physico-chemical profiles. Tertiary structure of proteins: use of molecular graphics and analysis softwares. Building of three-dimensional models of non-crystallized proteins at atomic detail, by means of the comparative modelling approach. Fold recognition and prediction methods. Energy minimization. Introduction to the molecular dynamics simulations and their applications. Introduction to the docking simulations for the study of the interaction between proteins and ligands.
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.
A. Tramontano, Integral and differential form of the protein folding problem, Physics of Life Reviews, 1:103-127 (2004).
W. L. Jorgensen, The many roles of computation in drug discovery, Science, 303:1813-1849 (2004).
Notes on the lessons will be given by the lecturer.
Teaching methodology: oral lectures and practical exercises by means of computer connected to the web.
Evaluation methodology: discussions on the reports of the practical exercises and oral examination.