We present a novel approach for studying the kinetics of protein folding. The framework has evolved from a robotics motion planning technique called probabilistic roadmap methods (prms) that has been applied in many
diverse fields with great success. In our previous work, we applied this method to study protein folding pathways
of several small proteins and obtained some very encouraging results.
In this paper, we describe how we applied our motion planning framework to the study of protein folding
kinetics. In particular, we present a refined version of our motion planning framework and describe how it can be
used to produce potential energy landscapes, free energy landscapes, and many folding pathways all from a single
roadmap which is computed in a few hours on a desktop PC. Results are presented for 14 proteins. Our ability
to produce large sets of unrelated folding pathways may potentially provide crucial insight into some aspects of
folding kinetics, such as proteins that exhibit both two-state and three-state kinetics, that are not captured by
other theoretical techniques.