M. Moll, D. Schwarz, and L. E. Kavraki, “Roadmap Methods for Protein Folding,” in Protein Structure Prediction: Methods and Protocols, Humana Press, 2007.
Protein folding refers to the process whereby a protein assumes its intricate three-dimensional shape. Different aspects of this problem have attracted much attention in the last decade. Both experimental and computational methods have been used to study protein folding and there has been considerable progress This chapter reviews a class of methods for studying protein folding called roadmap methods. These methods are relatively new and are still under active development. Roadmap methods are computational methods that have been developed to understand the process or the mechanism by which a protein folds or unfolds. It is typically assumed that the folded state is already known. Note that this is not a comprehensive survey of all existing computational protein folding methods. In particular, it does not cover Molecular Dynamics (MD) methods, Monte Carlo methods (MC), the use of coarse grain models in simulations and many others.