STRUCTURE-BASED DESIGN OF MODEL PROTEINS

A structure-based, sequence-design procedure is proposed in which one considers a set of decoy structures that compete significantly with th e target structure in being low energy conformations. The decoy struct ures are chosen to have strong overlaps in contacts with the putative native state, The procedure allows the design of sequences with large and small stability gaps in a random-bond heteropolymer model in both two and three dimensions by an appropriate assignment of the contact e nergies to both the native and nonnative contacts. The design procedur e is also successfully applied to the two-dimensional HP model. (C) 19 98 Wiley-Liss, Inc.