Folding pathways explored with artificial potential functions.

This paper considers the generation of trajectories to a given protein conformation and presents a novel approach based on artificial potential functions--originally proposed for multi-robot navigation. The artificial potential function corresponds to a simplified energy model, but with the novelty that--motivated by work on robotic navigation--a nonlinear compositional scheme of constructing the energy model is adapted instead of an additive formulation. The artificial potential naturally gives rise to a dynamic system for the protein structure that ensures collision-free motion to an equilibrium point.