Efficient construction of self-avoiding walks for protein folding simulations on a torus

摘要

Monte Carlo simulations of protein folding often have large running times because many generated conformations are not self-avoiding walks. This paper shows how a greater number of valid self-avoiding walks can be produced by first embedding a linear chain (representing a sequence of amino acids) into a binary n-cube and then embedding a torus into the n-cube to find the conformation. The described technique will permit analysis of both secondary and tertiary protein structures. (C) 1998 American Institute of Physics. [References: 15]