The Journal of Biological Physics and Chemistry

Possibility of using side chain orientation-based threading potential in fold recognition

B. Vishnepolsky, G. Managadze and M. Pirtskhalava*

Institute of Molecular Biology and Biological Physics, 12 Gotua St, 0160 Tbilisi, Georgia

The threading potential based on the side chain orientation of the C^α-C^β atoms in relation to their hydrophobic cores and on the distance of residues from the geometrical centre of the protein globule (ORDIS potential) has been constructed. The ORDIS potential enables structural similarity between remote homologies to be found better than using potentials based on evolutionary change data (BLOSUM ,PAM).

Keywords: fold recognition, side chain orientation, substitution matrix, threading.