Discrimination of native protein structures using atom-atom contact scoring.

ABSTRACT: We introduce a method for discriminating correctly folded proteins from well designed decoy structures using atom-atom and atom-solvent contact surfaces. The measure used to quantify contact surfaces integrates the solvent accessible surface and interatomic contacts into one quantity, allowing solvent to be treated as an atom contact. A scoring function was derived from statistical contact preferences within known protein structures and validated by using established protein decoy sets, including the "Rosetta" decoys and data from the CASP4 structure predictions. The scoring function effectively distinguished native structures from all corresponding decoys in >90% of the cases, using isolated protein subunits as target structures. If contacts between subunits within quaternary structures a

SUBMITTER: McConkey BJ 

PROVIDER: S-EPMC152272 | biostudies-literature | 2003 Mar

REPOSITORIES: biostudies-literature