Assessment of the quality of energy functions for protein folding by using a criterion derived with the help of the noisy go model.
We propose a simple criterion based on the Z-scoreto assess the quality of energy functions for protein folding: one should obtain Z>-10 for the equilibrium ensembleat about native conditions. We derive this criterionby studying a Go model with random errors added to the native interactions. The dependence of the Z-score on the thermodynamic parameters,including the noise, can be precisely obtained in this case,as the ground state of the model is known exactly.We apply this criterion to rapidly rule out two otherwise promisingpairwise energy approximations.The advantage of adopting the present criterionis that it is not necessary to know the ground state of an energy function to assess its quality. It is sufficient to compute the Z-scorefrom a single equilibrium simulation at around the folding temperature.
Oxford Centre for Molecular Sciences, New Chemistry Laboratory, University of Oxford, Oxford, OX1 3QT UK.
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Vendruscolo
Effective energy functions; Go model; Protein folding; Z-score