TCB Publications - Abstract

Peter L. Freddolino, Christopher B. Harrison, Yanxin Liu, and Klaus Schulten. Challenges in protein folding simulations. Nature Physics, 6:751-758, 2010. (PMC: 3032381)

FRED2010 Experimental studies of protein folding are hampered by the fact that only low resolution structural data can be obtained with sufficient temporal resolution. Molecular dynamics simulations offer a complementary approach, providing extremely high resolution spatial and temporal data on folding processes. However, such simulations are currently limited in several respects: the ability of molecular dynamics force fields to reproduce the true potential energy surfaces of proteins, the need of simulations to extend to the millisecond time scale of millisecond folding, and the difficulty of of sampling and analysis to capture the extremely heterogeneous folding processes and ongoing difficulties with obtaining sufficient sampling to meaningfully comment on folding mechanisms. We review recent progress in the simulation of three common model systems for protein folding, and discuss how advances in technology and theory are allowing protein folding simulations to address their current shortcomings.

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