Long-timescale molecular dynamics simulations of protein structure and function
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Long-timescale molecular dynamics simulations of protein structure and function. / Klepeis, John L; Lindorff-Larsen, Kresten; Dror, Ron O; Shaw, David E.
In: Current Opinion in Structural Biology, Vol. 19, No. 2, 2009, p. 120-7.Research output: Contribution to journal › Journal article › Research › peer-review
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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
VL - 19
SP - 120
EP - 127
JO - Current Opinion in Structural Biology
JF - Current Opinion in Structural Biology
SN - 0959-440X
IS - 2
ER -
ID: 37812379