Using motion planning to study protein folding pathways

In this paper we present a framework for studying protein folding pathways and potential landscapes which is based on Probabilistic Roadmap (prm) motion planning techniques which have proven to be very successful for problems involving high-dimensional conguration spaces. Our results applying prm techniques to several small proteins (approximately 60 residues) are very encouraging. The framework enables one to easily and eÆciently compute folding pathways from any denatured starting state to the native fold. This aspect makes our approach ideal for studying global properties of the protein's potential landscape. For example, our results show that folding pathways from dierent starting denatured states sometimes share some common 'gullies', mainly when they are close to the native fold. Such global issues are diÆcult to simulate and study with other methods. Our focus in this work is to study the protein folding mechanism assuming we know the native fold. Therefore, instead of performing fold prediction, we aim to study issues related to the folding process, such as the formation of secondary and tertiary structure, and the dependence on the initial conformation. Our results indicate that for some proteins, secondary structure clearly forms rs