Prediction of Protein Conformations by a Spin Glass Model (I)

Tsuyoshi Yoshizawa
Masaki Fumoto
Tamio Yasukawa

Division of Chemical and Biological Science and Technology, Faculty of Technology
Tokyo University of Agriculture and Technology
Nakamachi, Koganei, Tokyo 184, Japan


A spin glass model for polypeptide chains consisting of 4 states a, b, c and c , was introduced for the energy minimal conformation search by an extended Hopfield algorithm, in which energy dissipation rate was gradually reduced to simulate annealing processes. Inter-residue interaction energies were estimated by molecular mechanics program AMBER using model oligopeptide chains and crystal structure data. Preliminary results obtained with BPTI are not so satisfactory and several measures to improve the prediction accuracy were discussed.