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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