  We present a new method to extract distance and orientation dependent
potentials between amino acid side chains using a database of protein
structures and the standard Boltzmann device. The importance of orientation
dependent interactions is first established by computing orientational order
parameters for proteins with alpha-helical and beta-sheet architecture.
Extraction of the anisotropic interactions requires defining local reference
frames for each amino acid that uniquely determine the coordinates of the
neighboring residues. Using the local reference frames and histograms of the
radial and angular correlation functions for a standard set of non-homologue
protein structures, we construct the anisotropic pair potentials. The
performance of the orientation dependent potentials was studied using a large
database of decoy proteins. The results demonstrate that the new distance and
orientation dependent residue-residue potentials present a significantly
improved ability to recognize native folds from a set of native and decoy
protein structures.
