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.

中文翻译：

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DNA-DNA 和 DNA-蛋白质相互作用的分子动力学模拟。

全原子分子动力学方法可以以前所未有的分辨率表征 DNA 和 DNA-蛋白质系统中的分子级相互作用。计算技术的最新进展使该方法能够在微秒时间尺度上揭示此类系统的无偏行为，而增强采样方法已经足够成熟，可以以定量精度表征相互作用自由能。在这里，我们描述了通过改进分子动力学力场的准确性来提高此类模拟的真实性的最新进展，并强调了该方法在具有突出生物学意义的系统中的最新应用。