TY - JOUR
T1 - Path-sampling strategies for simulating rare events in biomolecular systems
AU - Chong, Lillian T.
AU - Saglam, Ali S.
AU - Zuckerman, Daniel M.
N1 - Publisher Copyright:
© 2016 Elsevier Ltd
PY - 2017/4/1
Y1 - 2017/4/1
N2 - Despite more than three decades of effort with molecular dynamics simulations, long-timescale (ms and beyond) biologically relevant phenomena remain out of reach in most systems of interest. This is largely because important transitions, such as conformational changes and (un)binding events, tend to be rare for conventional simulations (<10 μs). That is, conventional simulations will predominantly dwell in metastable states instead of making large transitions in complex biomolecular energy landscapes. In contrast, path sampling approaches focus computing effort specifically on transitions of interest. Such approaches have been in use for nearly 20 years in biomolecular systems and enabled the generation of pathways and calculation of rate constants for ms processes, including large protein conformational changes, protein folding, and protein (un)binding.
AB - Despite more than three decades of effort with molecular dynamics simulations, long-timescale (ms and beyond) biologically relevant phenomena remain out of reach in most systems of interest. This is largely because important transitions, such as conformational changes and (un)binding events, tend to be rare for conventional simulations (<10 μs). That is, conventional simulations will predominantly dwell in metastable states instead of making large transitions in complex biomolecular energy landscapes. In contrast, path sampling approaches focus computing effort specifically on transitions of interest. Such approaches have been in use for nearly 20 years in biomolecular systems and enabled the generation of pathways and calculation of rate constants for ms processes, including large protein conformational changes, protein folding, and protein (un)binding.
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U2 - 10.1016/j.sbi.2016.11.019
DO - 10.1016/j.sbi.2016.11.019
M3 - Review article
C2 - 27984811
AN - SCOPUS:85003918696
SN - 0959-440X
VL - 43
SP - 88
EP - 94
JO - Current Opinion in Structural Biology
JF - Current Opinion in Structural Biology
ER -