Simulating folding of helical proteins with coarse grained models

Abstract

We describe how potential parameters in a coarse graind model of proteins can be optimized with use of available protein three dimensional database. With this optimized potentials, we simulated a three helix bundle protein and found that all trajectories reach at the native structure within 1 microsecond. Interestingly, a quasi-mirror image is successfully discriminated from the native topology.