Seung-Gu Kang, Payel Das, et al.
Journal of Physical Chemistry B
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.
Seung-Gu Kang, Payel Das, et al.
Journal of Physical Chemistry B
Zaixing Yang, Peng Xiu, et al.
Journal of Physical Chemistry B
Cuicui Ge, Jian Tian, et al.
Archives of Toxicology
Weifeng Li, Ruhong Zhou, et al.
Journal of Physical Chemistry B