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 solvent accessible surface. To make computation feasible, we developed a new algorithm to compute the solvent accessible surface areas rapidly. 2) The supersecondary structures of each protein were predicted and used as restraints during the conformation searching processes. This algorithm was applied to five proteins. The overall fold of these proteins can be computed from their sequences, with deviations from crystal structures of 1.48–4.48 Å for C_α atoms. Proteins 31:247–257, 1998. © 1998 Wiley-Liss, Inc.