title: Challenges in protein folding simulations: Timescale, representation, and analysis.
abstract: Experimental studies of protein folding processes are frequently 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. The effectiveness of such simulations is currently hampered by continuing questions regarding the ability of molecular dynamics force fields to reproduce the true potential energy surfaces of proteins, 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 recent advances in technology and theory are allowing protein folding simulations to address their current shortcomings.
authors.affiliation: Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
authors.forename: Lydia
authors.initials: L
authors.lastname: Freddolino
authors.affiliation: Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
authors.forename: Christopher B
authors.initials: CB
authors.lastname: Harrison
authors.affiliation: Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801.|Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
authors.forename: Yanxin
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801.|Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
authors.forename: Klaus
authors.initials: K
authors.lastname: Schulten