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The analysis of coevolution of residues in homologous proteins is a powerfultool to predict their native conformation. The standard framework in whichcoevolutionary analysis is usually worked out is that of equilibrium Pottsmodels, assuming that proteins have evolved for enough time to reachthermodynamic equilibrium in sequence space. Here we propose a model todescribe correlations in sequences based on an explicit description of theevolutionary kinetics of proteins. We show that this procedure improves thecorrect prediction of native contacts with respect to equilibrium--basedmodels.

Prediction of native contacts in proteins from an out--of--equilibrium coevolutionary process