Molecular dynamics simulations of DNA-DNA and DNA-protein interactions.

Current Opinion in Structural Biology
Jejoong YooAleksei Aksimentiev

Abstract

The all-atom molecular dynamics method can characterize the molecular-level interactions in DNA and DNA-protein systems with unprecedented resolution. Recent advances in computational technologies have allowed the method to reveal the unbiased behavior of such systems at the microseconds time scale, whereas enhanced sampling approaches have matured enough to characterize the interaction free energy with quantitative precision. Here, we describe recent progress toward increasing the realism of such simulations by refining the accuracy of the molecular dynamics force field, and we highlight recent application of the method to systems of outstanding biological interest.

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Citations

Jan 13, 2021·Journal of Chemical Theory and Computation·Thomas J OweidaYaroslava G Yingling
May 1, 2021·International Journal of Molecular Sciences·Thomas CarzanigaTommaso Bellini
Jun 3, 2021·International Journal of Molecular Sciences·Neret Pujol-NavarroPaul Mulheran
Jun 18, 2021·The Journal of Physical Chemistry. B·Marina CorbellaShina Caroline Lynn Kamerlin
Oct 19, 2021·Journal of Chemical Theory and Computation·Korbinian Liebl, Martin Zacharias

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