Predicting the structures of 18 peptides using Geocore

We describe an extensive test of Geocore, an ab initio peptide folding algo rithm. We studied 18 short molecules for which there are structures in the Protein Data Bank; chains are up to 31 monomers long. Except for the very s hortest peptides, an extremely simple energy function is sufficient to disc riminate the true native state from more than 10(8) lowest energy conformat ions that are searched explicitly for each peptide. A high incidence of nat ive-like structures is found within the best few hundred conformations gene rated by Geocore for each amino acid sequence. Predictions improve when the number of discrete phi/psi choices is increased.