To milliseconds and beyond: challenges in the simulation of protein folding.

Lane TJ, Shukla D, Beauchamp KA, Pande VS.

Current Opinion in Structural Biology (Feb 2013)

The folding times accessible by simulation have increased exponentially over the past decade. Shown are all protein folding simulations conducted using unbiased, all-atom MD in empirical force-fields reported in the literature. Some folding times for the same protein differ, due to various mutations. FAH results are in blue, results from Shaw’s Anton supercomputer are in red.
This a review of protein folding achievement from Folding@home and other researchers. Our findings demonstrate that Folding@home is capable of simulating large, complex, and slow-folding proteins, beyond the capabilities of other systems, including the specialized hardware in the supercomputer from David Shaw’s DESRES group.

Quantitatively accurate all-atom molecular dynamics (MD) simulations of protein folding have long been considered a holy grail of computational biology. Due to the large system sizes and long timescales involved, such a pursuit was for many years computationally intractable. Further, sufficiently accurate forcefields needed to be developed in order to realistically model folding. This decade, however, saw the first reports of folding simulations describing kinetics on the order of milliseconds, placing many proteins firmly within reach of these methods. Progress in sampling and forcefield accuracy, however, presents a new challenge: how to turn huge MD datasets into scientific understanding. Here, we review recent progress in MD simulation techniques and show how the vast datasets generated by such techniques present new challenges for analysis. We critically discuss the state of the art, including reaction coordinate and Markov state model (MSM) methods, and provide a perspective for the future.