A Standard GA Approach to Native Protein Conformation Prediction

Abstract

Finding the 3-D geometry or tertiary structure of an arbitrary protein is vital to understanding the functionality of that protein. The prediction of this structure, known as the protein folding problem, is very difficult and has been labeled one of the "grand challenge problems" for the scientific community. We report here on further work to determine tertiary structures via genetic algorithms. We build on work done first by Unger and Moult using a simplified protein model but improve on the application of GAs to this model. We show, using the same simplified model, that the genetic algorithm indeed appears effective for determining tertiary structure with far fewer computational steps than first reported. 1. INTRODUCTION In this paper we explore the applicability of a standard GA approach to the problem of protein structure prediction. This section presents the problem of protein structure prediction in detail. For the reader with a basic understanding of biochemistry and the natur...