Spatial profiling of protein hydrophobicity: Native vs. Decoy structures

• DOI: 10.1002/prot.10419
• Publication Date: 2003-08-06T12:50:11Z
• Authors: Ruhong Zhou; B. David Silverman; Ajay K. Royyuru; Prasanna Athma
• Keywords: Decoy; Globular protein; Contact order; Hydrophobic effect

A recent study of 30 soluble globular protein structures revealed a quasi-invariant called the hydrophobic ratio. This invariant, which is ratio distance at second order moment vanished to zero vanished, was found be 0.75 +/- 0.05 for structures. report first describes results profiling 5,387 non-redundant domains Protein Data Bank, yields 0.71 0.08. Then, new score defined based on discriminate native-like proteins from decoy tested three widely used sets, namely Holm and Sander decoys, Park Levitt Baker decoys. Since characterizes global feature requires reasonably good statistics, this imposes constraint upon size in yield relatively smooth profiles. We show that even subject limitations (both & sets are small decoys), can provide useful information should complementary provided by force field calculations.