Biomedical subjects
Publications and source records attributed to Matteo Palassini.
We present a theoretical framework for characterizing the geometrical properties of the space of solutions in constraint satisfaction problems, together with practical algorithms for studying this structure on particular instances. We apply our method to the coloring problem, for which we obtain the total number of solutions and analyze in detail the distribution of distances between solutions.
We present a solvable model that predicts the folding kinetics of two-state proteins from their native structures. The model is based on conditional chain entropies. It assumes that folding processes are dominated by small-loop closure events that can be inferred from native structures. For CI2, the src SH3 domain, TNfn3, and protein L, the model reproduces two-state kinetics, and it predicts well the average Phi-values for secondary structures. The barrier to folding is the formation of predominantly local structures such as helices and hairpins, which are needed to bring nonlocal pairs of amino acids into contact.