Introduction -- Quantum chemical calculations for small protein models -- Car-Parrinello simulations of chemical reactions in proteins -- Strictly localised molecular orbitals in QM/MM methods -- Polarizable force fields for proteins -- Protein electrostatics -- Molecular mechanics/coarse-grained models -- Modelling the Dynamic Architecture of Biomaterials using Continuum Mechanics -- Structure prediction of transmembrane proteins -- Dynamics of small, folded proteins -- Protein Ligand Docking in Drug Discovery -- ADMET prediction based on protein structures -- Index.