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 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. (c) 2007 American Institute of Physics.