RIKEN Center for Computational Science, 6-7-1, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
RIKEN Center for Computational Science, 6-7-1, Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan; Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan.
Curr Opin Struct Biol. 2023 Oct;82:102653. doi: 10.1016/j.sbi.2023.102653. Epub 2023 Jul 12.
Flexible fitting based on molecular dynamics simulation is a technique for structure modeling from cryo-EM data. It has been utilized for nearly two decades, and while cryo-EM resolution has improved significantly, it remains a powerful approach that can provide structural and dynamical insights that are not directly accessible from experimental data alone. Molecular dynamics simulations provide a means to extract atomistic details of conformational changes that are encoded in cryo-EM data and can also assist in improving the quality of structural models. Additionally, molecular dynamics simulations enable the characterization of conformational heterogeneity in cryo-EM data. We will summarize the advancements made in these techniques and highlight recent developments in this field.
基于分子动力学模拟的柔性拟合是一种从冷冻电镜数据进行结构建模的技术。它已经被应用了近二十年，尽管冷冻电镜的分辨率有了显著提高，但它仍然是一种强大的方法，可以提供仅通过实验数据无法直接获得的结构和动力学见解。分子动力学模拟提供了一种从冷冻电镜数据中提取构象变化的原子细节的方法，也可以帮助提高结构模型的质量。此外，分子动力学模拟还可以用于描述冷冻电镜数据中的构象异质性。我们将总结这些技术的进展，并强调该领域的最新发展。
