[Folding@home] To milliseconds and beyond: challenges in the simulation of protein folding
Posted: Thu Dec 09, 2021 4:57 pm
Curr Opin Struct Biol. 2013 Feb;23(1):58-65. doi: 10.1016/j.sbi.2012.11.002. Epub 2012 Dec 10. ABSTRACT 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...
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