一个旋转模块库,使状折叠模块的建模和设计成为可能
P Douglas Renfrew1, Timothy W Craven, Glenn L Butterfoss
1Center for Genomics and Systems Biology, Department of Biology, ‡Department of Chemistry, and §Courant Institute of Mathematical Sciences, Computer Science Department, New York University , New York, New York 10003, United States.
Journal of the American Chemical Society
|May 15, 2014
概括
类,合成聚合物,现在可以通过计算建模复杂的仿生设计. 一个新的旋转器库准确地预测了类侧链结构,有助于设计新的折叠和功能.
科学领域:
- 合成化学 合成化学
- 计算生物学是一种计算生物学.
- 生物分子建模模型
背景情况:
- 类是具有可预测的二次结构的合成寡合物.
- 设计模仿生物分子的三级结构和功能仍然是一个挑战.
- 计算建模对于推进peptoid设计至关重要.
研究的目的:
- 开发准确的计算方法来预测peptoid形状.
- 为类侧链创建一个旋转器库.
- 为了使复杂的peptoid结构和功能的设计.
主要方法:
- 开发了一种用于类侧链形态和能量参数的计算方法.
- 计算了侧链形态状态的相对能量.
- 使用QM/MM方法为54个peptoid侧链创建了一个依赖于骨干 (BBD) 的旋转器库.
主要成果:
- 类侧链表现出旋转异构体,类似于蛋白质.
- 开发的旋转库准确地预测了类侧链的位置.
- 无论是QM还是MM的能量计算方法都被证明对rotamer图书馆开发有效.
结论:
- 计算方法和旋转器图书馆促进了准确的类模型建模.
- 这项工作使得能够设计具有特定三级结构和仿生功能的类动物.
- 将其纳入ROSETTA增强了其用于蛋白质和类设计的实用性.
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