Statistical Mechanics Approach to Protein Design

The plan of this thesis is the following. In the first chapter we introduce the most important and basic concept related to protein folding and design. In the second chapter, after introducing some standard lattice models of proteins and heteropolymers, the most important methods of protein design present in the literature are described. In the third chapter we will introduce a novel iterative procedure for protein design and it will be applied to lattice protein models [58]. A different approach based on geometrical criterion [49] will also be presented. In the fourth chapter, we will implement an approximated approach in order to design real protein structures [59]. In this case, it has been possible to compare our designed sequences with real sequences, whose native states are known. The good correlation between natural sequences and designed sequences indicates that the method is very promising.