  The analysis of coevolution of residues in homologous proteins is a powerful
tool to predict their native conformation. The standard framework in which
coevolutionary analysis is usually worked out is that of equilibrium Potts
models, assuming that proteins have evolved for enough time to reach
thermodynamic equilibrium in sequence space. Here we propose a model to
describe correlations in sequences based on an explicit description of the
evolutionary kinetics of proteins. We show that this procedure improves the
correct prediction of native contacts with respect to equilibrium--based
models.
