Dihedral angle principal component analysis of molecular dynamics simulations
Dihedral angle principal component analysis of molecular dynamics simulations
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DOI：
10.1063/1.2746330
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发表时间：
2007-06-28
影响因子：
4.4
通讯作者：
Stock, Gerhard
中科院分区：
文献类型：
--
作者：
Altis, Alexandros;Nguyen, Phuong H.;Stock, Gerhard
Mu [Proteins 58，45（2005）]最近建议在分子动力学模拟的主成分分析中使用骨架二面角代替笛卡尔坐标。二面角可能是有利的，因为内部坐标自然地提供了内部和整体运动的正确分离，这被发现对于经历大结构重排的生物分子的自由能景观的构建和解释是必不可少的。为了说明角变量的圆形统计，采用从二面角空间{phi（n）}到度量坐标空间{x（n）=cos phi（n），y（n）=sin phi（n）}的变换。为了研究该方法的有效性和适用性，在这项工作中的二面角主成分分析（dPCA）的理论基础进行了讨论。结果表明，dPCA相当于一个一对一的原始角度分布的代表，其主要成分可以很容易地由相应的构象变化的肽的特征。此外，介绍了一个复杂版本的dPCA，其中N个角度变量自然导致N个特征值和特征向量。应用该方法从300 ns的分子动力学模拟十丙氨酸的自由能景观的建设，各种方法的关键比较。(c)2007年，美国物理学会。
It has recently been suggested by Mu [Proteins 58, 45 (2005)] to use backbone dihedral angles instead of Cartesian coordinates in a principal component analysis of molecular dynamics simulations. Dihedral angles may be advantageous because internal coordinates naturally provide a correct separation of internal and overall motion, which was found to be essential for the construction and interpretation of the free energy landscape of a biomolecule undergoing large structural rearrangements. To account for the circular statistics of angular variables, a transformation from the space of dihedral angles {phi(n)} to the metric coordinate space {x(n)=cos phi(n),y(n)=sin phi(n)} was employed. To study the validity and the applicability of the approach, in this work the theoretical foundations underlying the dihedral angle principal component analysis (dPCA) are discussed. It is shown that the dPCA amounts to a one-to-one representation of the original angle distribution and that its principal components can readily be characterized by the corresponding conformational changes of the peptide. Furthermore, a complex version of the dPCA is introduced, in which N angular variables naturally lead to N eigenvalues and eigenvectors. Applying the methodology to the construction of the free energy landscape of decaalanine from a 300 ns molecular dynamics simulation, a critical comparison of the various methods is given. (c) 2007 American Institute of Physics.