The ugly, bad, and good stories of large-scale biomolecular simulations
The ugly, bad, and good stories of large-scale biomolecular simulations
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DOI：
10.1016/j.sbi.2022.102338
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发表时间：
2022-03-01
影响因子：
6.8
通讯作者：
Singharoy, Abhishek
中科院分区：
文献类型：
--
作者：
Gupta, Chitrak;Sarkar, Daipayan;Singharoy, Abhishek
大型生物分子组装的分子建模例证了一个既有希望又有争议的颠覆性领域。在善待动物组织和艾斯卡计算的推动下，几种模拟方法现在已经成熟为用户友好的工具，成功地用于模拟病毒、膜性纳米结构和遗传机制的关键部件。我们提出了三个统一的生物物理主题，这些主题源于最近的一些数百万原子模拟努力。尽管将分子变化与表型结果联系起来，但这些模拟的质量衡量标准仍然值得怀疑。我们讨论了现有的和即将出现的构建具有代表性的大系统系综的策略，以及新的计算技术将如何推动这一领域的发展，并指出以实验数据为指导的综合建模是生物分子计算的未来。
Molecular modeling of large biomolecular assemblies exemplifies a disruptive area holding both promises and contentions. Propelled by peta and exascale computing, several simulation methodologies have now matured into user-friendly tools that are successfully employed for modeling viruses, membranous nano-constructs, and key pieces of the genetic machinery. We present three unifying biophysical themes that emanate from some of the most recent multi-million atom simulation endeavors. Despite connecting molecular changes with phenotypic outcomes, the quality measures of these simulations remain questionable. We discuss the existing and up-coming strategies for constructing representative ensembles of large systems, how new computing technologies will boost this area, and make a point that integrative modeling guided by experimental data is the future of biomolecular computations.