Toward a Monte Carlo simulation of protein systems in amino-acid sequence space

Abstract

In this article, we present our strategy for studying amino-acid sequence dependences on protein structures. For this purpose, performing Metropolis Monte Carlo simulations in the amino-acid sequence space is necessary. We want to use a coarse-grained protein model with an accurate potential energy function. We introduce a method for optimizing potential-energy parameters based on the native protein structure database, Protein Data Bank.