Folding simulations with novel conformational search method.

A novel scheme for fast conformational search has been developed by combining the replica exchange method (REM) with the generalized effective potential concept. The new method, referred to Q-REM [S. Jang et al. Phys. Rev. Lett. 91, 058305 (2003)], is expected to provide a useful alternative to the conventional REM for effective conformational sampling of complex systems. The authors have performed folding simulations of the Trp-cage miniprotein using Q-REM. All atom level simulations with generalized Born solvent access-area solvation model show that successful folding can be observed with much smaller number of replicas in Q-REM compared to the conventional REM. It can be concluded that the new method has potential to significantly improve sampling efficiency, allowing simulations of more challenging systems.