关于EMDataResource Cryo-EM Ligand 建模挑战的结果
Catherine L Lawson1, Andriy Kryshtafovych2, Grigore D Pintilie3
1Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
Research square
|February 12, 2024
概括
在EMDataResource的联结体模型挑战中发现,在近原子分辨率的冷电磁图中评估联结体模型需要多个分数. 建议使用最佳实践来评估这些巨分子+连接体结构.
科学领域:
- 结构生物学 结构生物学
- 生物化学 生物化学
- 生物物理学的生物物理.
背景情况:
- 低温电子显微镜 (cryo-EM) 正在取得接近原子分辨率的进展.
- 准确地建模与宏分子结合的连接物对于理解生物功能至关重要.
- 评估这些联结体模型的质量是一个挑战.
研究的目的:
- 在近原子分辨率的冷电磁图中评估连接体建模的可靠性和可重复性.
- 确定在冷EM中评估宏分子-连接体复合物的最佳实践.
- 为了对当前的连接物建模方法进行基准测试.
主要方法:
- 在EMDataResource 带模型挑战中,使用了三个已发表的冷电磁图 (1.9-2.5 Å分辨率) 作为目标.
- 17个独立研究小组提交了61个配体模型.
- 模型使用视觉检查,局部地图质量,模型与地图相匹配,几何,能量和接触分数进行评估.
主要成果:
- 提交的连接体模型和周围原子的质量差异很大.
- 没有单一的评分指标是足够的;综合得分是必要的全面评估.
- 模型与地图相匹配和几何质量是关键指标,但能源和联系也发挥了作用.
结论:
- 目前在近原子分辨率的冷EM中对连接体进行建模是可变的.
- 结合各种评分指标的多面性方法对于可靠的质量评估至关重要.
- 提供了关于结合性宏分子的冷EM结构验证的最佳实践建议.
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