Dynamical equation approach to protein design

Abstract

A new approach to protein design is proposed. Our dynamical equation approach is based on the criterion by Kurosky and Deutsch, 1), 2) with which the probability of a target structure in a conformation space is maximized at low but finite temperature. The key feature of the proposed approach is soft spin representation of monomer variables that leads to the "design equation".3) The advantage of the present approach is its parallel evolution of the monomer sequence variables and the resulting rapid convergence. We review the recent development of design schemes, implement numerical simulations by the design equation for the generalized HP model, 24), 26), 27) and compare the performance with an algorithm based on the simulated annealing in sequence space.