<P> For the most part, scientists have been able to study many identical molecules folding together en masse . At the coarsest level, it appears that in transitioning to the native state, a given amino acid sequence takes roughly the same route and proceeds through roughly the same intermediates and transition states . Often folding involves first the establishment of regular secondary and supersecondary structures, in particular alpha helices and beta sheets, and afterward tertiary structure . </P> <P> De novo or ab initio techniques for computational protein structure prediction are related to, but strictly distinct from, experimental studies of protein folding . Molecular Dynamics (MD) is an important tool for studying protein folding and dynamics in silico . First equilibrium folding simulations were done using implicit solvent model and umbrella sampling . Because of computational cost, ab initio MD folding simulations with explicit water are limited to peptides and very small proteins . MD simulations of larger proteins remain restricted to dynamics of the experimental structure or its high - temperature unfolding . Long - time folding processes (beyond about 1 millisecond), like folding of small - size proteins (about 50 residues) or larger, can be accessed using coarse - grained models . </P> <P> The 100 - petaFLOP distributed computing project Folding@home created by Vijay Pande's group at Stanford University simulates protein folding using the idle processing time of CPUs and GPUs of personal computers from volunteers . The project aims to understand protein misfolding and accelerate drug design for disease research . </P> <P> Long continuous - trajectory simulations have been performed on Anton, a massively parallel supercomputer designed and built around custom ASICs and interconnects by D.E. Shaw Research . The longest published result of a simulation performed using Anton is a 2.936 millisecond simulation of NTL9 at 355 K . </P>

How a protein folds in accordance with an emerging amino-acid sequence