Paper Citing NAMD - Abstract
Cruzeiro, Leonor; Lopes, Paulo A.
Are the native states of proteins kinetic traps?
MOLECULAR PHYSICS, 107:1485-1493, 2009
Four proteins were selected to represent each of the four different CATH classes and, for each protein, three decoys were constructed with structures totally alien to the native state. The decoys were scored against the native state with the help of the AMBER force field, using three measures: the average energy, the average fluctuation and the resistance to a heat pulse. Two sets of simulations were performed, one with explicit solvent and the other with implicit solvent. The overall conclusion is that, of these three measures, the most successful in picking out the native states was the last one, since the native structures take a consistently longer time to be destabilized in this manner. However, the general conclusion is also that none of the measures is completely effective in discriminating all the decoys, a result that supports other studies, according to which the native state is reached by a kinetic step.
