Simulating the Folding of Proteins

.......................................................................................................................................... 3 Introduction ..................................................................................................................................... 4 Protein Structure .......................................................................................................................... 4 Protein Thermodynamics ............................................................................................................ 6 Predicting the Conformation of a Protein ................................................................................... 7 Genetic Algorithms ..................................................................................................................... 7 Methodology ................................................................................................................................... 8 Determining Atom Positions in Cartesian Coordinates .............................................................. 9 Protein Energy Function............................................................................................................ 10 Internal Energy ...................................................................................................................... 10 Electrostatic Solvation Energy .............................................................................................. 10 Nonpolar Solvation Energy ................................................................................................... 13 Optimization Methods ............................................................................................................... 14 Gradient Search ..................................................................................................................... 14 Golden Search ....................................................................................................................... 15 Genetic Algorithm ..................................................................................................................... 15 Initialization .......................................................................................................................... 15 Selection ................................................................................................................................ 15 Reproduction ......................................................................................................................... 15 Mutation ................................................................................................................................ 16 Termination ........................................................................................................................... 17 Local Optimization Results ........................................................................................................... 17 Computation Time..................................................................................................................... 17