Protein structure prediction by an iterative search method

Ivan C. Rankenburg and Veit Elser Abstract We demonstrate a new algorithm for finding protein conformations that minimize a non-bonded energy function. The new algorithm, called the difference map, seeks to find an atomic configuration that is simultaneously in two constraint spaces. The first constraint space is the space of atomic configurations that have a valid peptide geometry, while the second is the space of configurations that have a non-bonded energy below a given target. These two constraint spaces are used to define a deterministic dynamical system, whose fixed points produce atomic configurations in the intersection of the two constraint spaces. The rate at which the difference map produces low energy protein conformations is compared with that of a contemporary search algorithm, parallel tempering. The results indicate the difference map finds low energy protein conformations at a significantly higher rate then parallel tempering.