Ab Initio Protein Folding Using a Cooperative Swarm of Molecular Dynamics Trajectories

The use of atomistic simulation techniques to directly resolve the protein tertiary structure from the primary amino acid sequence is hindered by the rough topology of the protein free energy surface and the resulting simulation time scales required. We explore here the use of a molecular dynamics technique based on swarm intelligence to identify the native states of two peptides and a Trp-cage miniprotein. In all cases, the presence of cooperative swarm interactions significantly enhanced the efficiency of molecular dynamics simulations in predicting the native conformation.