Abstract
In this paper, an improved Ca-SC energy potential designed for protein fold recognition was reported. It
consists of three extremely simple interaction terms which are supposed to be the dominant interactions
in protein folding: residue–residue contact, hydrophobicity and pseudodihedral potentials. The potential
function only contains 210 contacts, one hydrophobic and one torsion parameters, which have been optimized
using an interior point algorithm of linear programming. Tests of the derived potential function on
commonly used decoy sets illustrate that it outperforms most of the existing coarse-grained potentials in
terms of its capabilities in recognizing native structures and consistency in achieving high Z-scores across
decoy sets, and it has almost equivalent performance to the potentials which considered complex intramolecular
interactions. The results show that our scoring function is a generally prospective potential for
protein structure prediction and modeling with regard to its recognition and computation efficacy.