Detecting native protein folds among large decoy sets with hydrophobic moment profiling.

Abstract

A new hydrophobic score will be presented in this paper for detecting native-like folds from a large set of decoy structures. A recent paper (B. D. Silverman, PNAS 98, 4996, 2001) had revealed that for globular proteins there exists a relatively universal constant of 0.74 for a hydrophobic ratio, which is defined as the ratio of radii from the protein centroid at which the second order hydrophobic moment and the zero order moment vanishes. This paper further defines a new hydrophobic score which will be used to examine protein decoys, in particular, the Holm & Sander, Park & Levitt and Baker decoy sets. It will be shown that the hydrophobic score and profile shapes can provide useful information that should be complementary to the information provided by other procedures, such as free energy calculations.