Spectroscopic Methods
Absorption spectroscopy: basic principles, spectroscopic analysis of biopolymers, absorption and conformation. Optical activity. Rotatory optical dispersion and circular dichroism: application to biological systems. Fluorescence spectroscopy: basic principles, fluorescence intensity, fluorophores, fluorescence resonance energy transfer (FRET) as spectroscopic ruler, fluorescence anisotropy. Case studies in fluorescence spectroscopy of biomolecules. NMR Spectroscopy: basic concepts, analysis of 1D NMR spectra. 2D and ND NMR spectroscopy: experiments and applications to solve protein structure and dynamics. Computational methods to determine 3D structure from NMR data.

Computational Methods
Introduction: molecular models, 3D representation of the molecules. Data Banks of molecular structures: Cambridge Structural Database, Protein Databank.
Molecular Mechanics: force fields, potential energy of biological macromolecules, methods of energy minimization for the exploration of the potential energy surface.
Molecular dynamics: temporal evolution of molecular models. Molecular dynamics simulation at constant pressure and temperature. Analysis of the trajectories for the calculation of structural and dynamic properties of macromolecular systems. Conformational analysis of biomacromolecules. Rational design of bioactive molecules by using computational methods. Molecular dynamics simulation of proteins, biological membranes, membrane proteins and nucleic acids.

Cantor and Schimmel: Biopysical Chemistry Parts I, II and III. W.H Freeman and Company, San Francisco CA.
Freifelder, D., Physical Biochemistry, W.H Freeman and Company, New York.
•T. E. Creighton, Proteins: Structures and Molecular Properties. W.H Freeman and Company, New York.
J. Cavanagh,W.J. Fairbrother, A.G. PalmerIII, N.J. Skelton, Protein NMR Spectroscopy:Principles and Practice, Academic Press, inc.
A. Leach Molecular Modelling: Principles and Applications. Prentice Hall; 2 Ed
H. D. Höltje, W. Sippl, Didier Rognan, G. Folkers Molecular Modeling; Basic Principles and Applications. Wiley-VCH
S. Pascarella, A. Paiardini Bioinformatica: Dalla sequenza alla struttura delle proteine. Zanichelli

Introduction: molecular models, 3D representation of the molecules. Data Banks of molecular structures: Cambridge Structural Database, Protein Databank.
Molecular Mechanics: force fields, potential energy of biological macromolecules, methods of energy minimization for the exploration of the potential energy surface.
Molecular dynamics: temporal evolution of molecular models. Molecular dynamics simulation at constant pressure and temperature. Analysis of the trajectories for the calculation of structural and dynamic properties of macromolecular systems. Conformational analysis of biomacromolecules. Rational design of bioactive molecules by using computational methods. Molecular dynamics simulation of proteins, biological membranes, membrane proteins and nucleic acids.

A. Leach Molecular Modelling: Principles and Applications. Prentice Hall; 2 Ed
H. D. Höltje, W. Sippl, Didier Rognan, G. Folkers Molecular Modeling; Basic Principles and Applications. Wiley-VCH
K. E. van Holde, W. C. Johnson, P. S. Ho Priciples of Physical Biochemistry. Prentice-Hall (2005)