What should the Z-score of native protein structures be?
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.
Zhang
L
L
Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
Skolnick
J
J
D008956:Models, Chemical; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
D011506:Proteins