Protein tertiary structure predictions by Monte Carlo simulations

Abstract

Predictions of protein tertiary structures are carried out by Monte Carlo simulations. Our approach consists of two aspects: the inclusion of accurate solvent effects and the development of powerful simulation algorithms that can avoid getting trapped in states of energy local minima. For the former, we discuss several models varying in nature from crude (distancedependent dielectric function) to rigorous (reference interaction site model). For the latter, we show the effectiveness of Monte Carlo simulated annealing and generalized-ensemble algorithms.