Long-timescale molecular dynamics simulations of protein structure and function

TY - JOUR

T1 - Long-timescale molecular dynamics simulations of protein structure and function

AU - Klepeis, John L

AU - Lindorff-Larsen, Kresten

AU - Dror, Ron O

AU - Shaw, David E

PY - 2009

Y1 - 2009

N2 - Molecular dynamics simulations allow for atomic-level characterization of biomolecular processes such as the conformational transitions associated with protein function. The computational demands of such simulations, however, have historically prevented them from reaching the microsecond and greater timescales on which these events often occur. Recent advances in algorithms, software, and computer hardware have made microsecond-timescale simulations with tens of thousands of atoms practical, with millisecond-timescale simulations on the horizon. This review outlines these advances in high-performance molecular dynamics simulation and discusses recent applications to studies of protein dynamics and function as well as experimental validation of the underlying computational models.

AB - Molecular dynamics simulations allow for atomic-level characterization of biomolecular processes such as the conformational transitions associated with protein function. The computational demands of such simulations, however, have historically prevented them from reaching the microsecond and greater timescales on which these events often occur. Recent advances in algorithms, software, and computer hardware have made microsecond-timescale simulations with tens of thousands of atoms practical, with millisecond-timescale simulations on the horizon. This review outlines these advances in high-performance molecular dynamics simulation and discusses recent applications to studies of protein dynamics and function as well as experimental validation of the underlying computational models.

U2 - 10.1016/j.sbi.2009.03.004

DO - 10.1016/j.sbi.2009.03.004

M3 - Journal article

C2 - 19361980

SN - 0959-440X

VL - 19

SP - 120

EP - 127

JO - Current Opinion in Structural Biology

JF - Current Opinion in Structural Biology

IS - 2

ER -