Approccio montecarlo al protein design

Protein coevolution and the affinity maturation process of antibodies (Abs) both work in an evolutionary like fashion and Multivariate Gaussian Modelling (MGM), developed in [19], has already been proven to be fast and very efficient (i) in detecting residue-residue contacts in proteins and (ii) in scoring the neutralization power of the Abs targeted to a specific antigen [18]. In this thesis we use the statistical energy derived from MGM inferred on a multiple sequence alignment (MSA) to develop a tool able to generate completely new protein sequences designed to have the same statistical features of the sequences belonging to the starting MSA. This means designing new proteins with structure and function similar to the starting ones, in the case of a MSA composed of homologous proteins, or with high neutralization power toward an antigen, in the case of a MSA composed of Abs targeted to it. The result is a useful parameter setting for the statistical energy, that could also be used to score the sequences belonging to a particular MSA.