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Protein Science, Vol 7, Issue 5 1201-1207, Copyright © 1998 by Cold Spring Harbor Laboratory Press

ARTICLE

What should the Z-score of native protein structures be?

L. ZHANG and J. SKOLNICK
Department of Molecular Biology, TPC-5, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037

The Z-score of a protein is defined as the energy separation between the native fold and the average of an ensemble of misfolds in the units of the standard deviation of the ensemble. The Z-score is often used as a way of testing the knowledge-based potentials for their ability to recognize the native fold from other alternatives. However, it is not known what range of values the Z-scores should have if one had a correct potential. Here, we offer an estimate of Z-scores extracted from calorimetric measurements of proteins. The energies obtained from these experimental data are compared with those from computer simulations of a lattice model protein. It is suggested that the Z-scores calculated from different knowledge-based potentials are generally too small in comparison with the experimental values.
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