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

The results of an optimization of a folding potential are reported. The com plete energy function is modeled as a sum of pairwise interactions with a f lexible functional form. The relevant distance between two amino acids (2 - 9 Angstrom) 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 2999;49:71-85) that it is impossible to find a pair p otential with the above flexible form that recognizes all native folds. Nev ertheless, a potential that rates correctly a subset of the decoy structure s was constructed and optimized. The resulting potential is compared with a distance-dependent statistical potential of Bahar and Jernigan. It is furt her tested against decoy structures that were created in the Levitt's group . On average, the new potential places native shapes lower in energy and pr ovides higher Z scores than other potentials. Proteins 2000; 41:40-46. (C) 2000 Wiley-Liss, Inc.