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

✍ Scribed by Li Zhang; Jeffrey Skolnick

• Publisher: Cold Spring Harbor Laboratory Press
• Year: 1998
• Tongue: English
• Weight: 598 KB
• Volume: 7
• Category: Article
• ISSN: 0961-8368
• DOI: 10.1002/pro.5560070515

✦ Synopsis

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.