PROTEIN-FOLDING SIMULATION WITH GENETIC ALGORITHM AND SUPERSECONDARY STRUCTURE CONSTRAINTS

We describe an algorithm to compute native structures of proteins from their primary sequences. The novel aspects of this method are: 1) The hydrophobic potential was set to be proportional to the nonpolar solv ent accessible surface. To make computation feasible, we developed a n ew algorithm to compute the solvent accessible surface areas rapidly. 2) The supersecondary structures of each protein were predicted and us ed as restraints during the conformation searching processes, This alg orithm was applied to five proteins. The overall fold of these protein s can be computed from their sequences, with deviations from crystal s tructures of 1.48-4.48 Angstrom for C-alpha atoms. (C) 1998 Wiley-Liss , Inc.