(1) Faculty of Chemistry, University of Gdańsk, ul. Sobieskiego 18, 80-952 Gdańsk, Poland, PL;(2) Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA, US
Abstract:
A united-residue model of polypeptide chains developed in our laboratories with united side-chains and united peptide groups
as interaction sites is presented. The model is designed to work in continuous space; hence efficient global-optimization
methods can be applied. In this work, we adopted the distance-scaling method that is based on continuous deformation of the original
rugged energy hypersurface to obtain a smoothed surface. The method has been applied successfully to predict the structures
of simple motifs, such as the three-helix bundle structure of the 10-58 fragment of staphylococcal protein A in de novo folding
simulations and more complicated motifs in inverse-folding simulations.
Received: 24 April 1998 / Accepted: 4 August 1998 / Published online: 2 November 1998