Protein Folding Implementation of the Simulated Annealing Algorithm on Simple Three-Dimensional Models

摘要

How an arbitrary coil of amino acids folds into its functional structure is known asthe protein folding problem. Since the underlying mechanisms that guide proteinfolding in nature are widely unknown, simpli ed models are studied. Many of thesemodels have energy levels as the focal point in order to nd the native state andmay ignore other relevant constraints. While these simpli ed models may seem tootrivial to have any resemblance to the physical reality, they can be used to exploreconcepts and ideas that may lead to further insights on how proteins fold.This thesis studies the use of simulated annealing optimization techniques to findlow energy states in simple lattice and off-lattice models. A certain emphasis isplaced upon looking for patterns in the results emerging. One simple off -latticemodel and two lattice models are considered, a cubic lattice and a face-centeredcubic lattice. Compared to the optimal energy, low energy conformations of 48-residue chains are found in reasonable time. It is concluded that while the methodcan not be said to exhibit the behavior of nding one consistent native state eachtime it is run, patterns do emerge in the results.