Importance of long-time simulations for rare event sampling in zinc finger proteins

Journal of Biomolecular Structure & Dynamics
Ryan GodwinFreddie R Salsbury

Abstract

Molecular dynamics (MD) simulation methods have seen significant improvement since their inception in the late 1950s. Constraints of simulation size and duration that once impeded the field have lessened with the advent of better algorithms, faster processors, and parallel computing. With newer techniques and hardware available, MD simulations of more biologically relevant timescales can now sample a broader range of conformational and dynamical changes including rare events. One concern in the literature has been under which circumstances it is sufficient to perform many shorter timescale simulations and under which circumstances fewer longer simulations are necessary. Herein, our simulations of the zinc finger NEMO (2JVX) using multiple simulations of length 15, 30, 1000, and 3000 ns are analyzed to provide clarity on this point.

References

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Jan 3, 2012·Journal of Biomolecular Structure & Dynamics·Lacramioara Negureanu, Freddie R Salsbury
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Citations

Nov 1, 2016·Journal of Biomolecular Structure & Dynamics·Jiajie Xiao, Freddie R Salsbury
Feb 24, 2018·Journal of Biomolecular Structure & Dynamics·Jiajie XiaoFreddie R Salsbury
Aug 18, 2017·Journal of Biomolecular Structure & Dynamics·Ryan C GodwinFreddie R Salsbury
Aug 12, 2017·Protein Science : a Publication of the Protein Society·Ryan L MelvinFreddie R Salsbury
Sep 27, 2018·Physical Review. E·Ryan L MelvinFreddie R Salsbury
Jan 16, 2021·Journal of Chemical Information and Modeling·Dizhou WuFreddie R Salsbury
Nov 2, 2016·Journal of Chemical Theory and Computation·Ryan L MelvinFreddie R Salsbury
Sep 19, 2019·Journal of Chemical Information and Modeling·Roy González-AlemánLuis A Montero-Cabrera

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Methods Mentioned

BETA
protein folding
NMR

Software Mentioned

visual dynamics VMD
ACEMD
Acellera
CHARMM
NEMO

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