Distance-dependent, pair potential for protein folding: results from linear optimization

The results of an optimization of a folding potential are reported. The complete energy function is modeled as a sum of pairwise interactions with a flexible functional form. The relevant distance between two amino acids (2 - 9 A) is divided into 13 intervals, and the energy of each interval is optimized independently. We show, in accord with a previous publication (Tobi et al., Proteins 2000;40:71-85) that it is impossible to find a pair potential with the above flexible form that recognizes all native folds. Nevertheless, a potential that rates correctly a subset of the decoy structures was constructed and optimized. The resulting potential is compared with a distance-dependent statistical potential of Bahar and Jernigan. It is further tested against decoy structures that were created in the Levitt's group. On average, the new potential places native shapes lower in energy and provides higher Z scores than other potentials.