  Natural proteins fold to a unique, thermodynamically dominant state. Modeling
of the folding process and prediction of the native fold of proteins are two
major unsolved problems in biophysics. Here, we show successful all-atom ab
initio folding of a representative diverse set of proteins, using a minimalist
transferable energy model that consists of two-body atom-atom interactions,
hydrogen-bonding, and a local sequence energy term that models
sequence-specific chain stiffness. Starting from a random coil, the native-like
structure was observed during replica exchange Monte Carlo (REMC) simulation
for most proteins regardless of their structural classes; the lowest energy
structure was close to native- in the range of 2-6 A root-mean-square deviation
(RMSD). Our results demonstrate that the successful all-atom folding of a
protein chain to its native state is governed by only a few crucial energetic
terms.
