On the accuracy of metadynamics and its variations in a protein folding process
On the accuracy of metadynamics and its variations in a protein folding process
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关于蛋白质折叠过程中元动力学的准确性及其变化
DOI：
10.1080/08927022.2014.931680
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发表时间：
2015-06-13
影响因子：
2.1
通讯作者：
Wang, Wei
中科院分区：
文献类型：
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作者：
Bian, Yunqiang;Zhang, Jian;Wang, Wei
形而上学及其变体是探索物理、化学和生物物理系统的自由能景观的强大工具。然而，以前的测试，他们的准确性是基于低维系统或复杂的系统没有确切的答案。因此，它们的准确性，特别是当用于高维生物物理系统时，还没有经过严格的测试。在这项工作中，我们进行了一系列的模拟与metadaptics及其变化的一个典型的生物物理过程-蛋白质糜蛋白酶抑制剂2（CI 2）的折叠基于粗粒度的结构为基础的模型。结果揭示了算法的能力和局限性，并为在高维生物系统中使用元adaptics及其变体提供了一些指导。
Metadynamics and its variations are powerful tools for exploring the free energy landscape of physical, chemical and biophysical systems. However, previous tests of their accuracy were based on either low-dimensional systems or complicated systems without exact answers. Therefore their accuracy, particularly when used for high-dimensional biophysical systems, has not been rigorously tested. In this work we performed a series of simulations with metadynamics and its variations for a typical biophysical process – the folding of protein chymotrypsin inhibitor 2 (CI2) based on a coarse-grained structure-based model. The results revealed the power as well as limitations of the algorithms and provided some guidelines for using metadynamics and its variations in high-dimensional biological systems.