Simple Models of Protein Folding

Lattice models with simplified interaction potentials have been used to analyze the ability of certain amino acid sequences to adopt a unique configuration in space [1, 2, 3]. Furthermore, phenomenological models have been used to predict protein folding kinetics amongst a subset of energetically favorable states [4, 5]. In the following, I will specifically discuss both the use of two dimensional lattice models and simple rate matrices to describe the transition of disordered proteins to a unique native state (or subset of states). Furthermore, I will discuss the use of both molecular dynamics simulations and experimental techniques to observe specific pathways for protein folding and provide direct connections to theory.