Evaluation of Dimensionality-reduction Methods from Peptide Folding-unfolding Simulations.
Evaluation of Dimensionality-reduction Methods from Peptide Folding-unfolding Simulations.
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DOI：
10.1021/ct400052y
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发表时间：
2013-05-14
影响因子：
5.5
通讯作者：
Huo, Shuanghong
中科院分区：
文献类型：
--
作者：
Duan, Mojie;Fan, Jue;Li, Minghai;Han, Li;Huo, Shuanghong
非线性约化方法已被广泛用于研究分子体系的自由能景观和低自由能途径。结果表明，在一些简单的系统中，非线性降维方法比线性方法（如主成分分析）具有更好的嵌入效果。在这项研究中，我们评估了几种非线性方法，局部线性嵌入，Isomap，和扩散图，以及主成分分析从平衡折叠/解折叠轨迹的链球菌蛋白G的B1结构域的第二个β-发夹。使用CHARMM parm19极性氢势函数。采用一系列反映包埋质量不同方面的标准进行评价。我们的结果表明，主成分分析是不差于非线性的这个复杂的系统。在评价的各个方面都没有明确的赢家。每种降维方法都有其局限性。我们强调，对嵌入结果进行公平、信息丰富的评估需要多种评估标准的组合，而不是任何单一标准。当使用降维方法时，特别是当仅使用少数几个顶部嵌入维度来描述自由能景观时，应谨慎使用。
Dimensionality reduction methods have been widely used to study the free energy landscapes and low-free energy pathways of molecular systems. It was shown that the non-linear dimensionality-reduction methods gave better embedding results than the linear methods, such as principal component analysis, in some simple systems. In this study, we have evaluated several non linear methods, locally linear embedding, Isomap, and diffusion maps, as well as principal component analysis from the equilibrium folding/unfolding trajectory of the second β–hairpin of the B1 domain of streptococcal protein G. The CHARMM parm19 polar hydrogen potential function was used. A series of criteria which reflects different aspects of the embedding qualities were employed in the evaluation. Our results show that principal component analysis is not worse than the non-linear ones on this complex system. There is no clear winner in all aspects of the evaluation. Each dimensionality-reduction method has its limitations in a certain aspect. We emphasize that a fair, informative assessment of an embedding result requires a combination of multiple evaluation criteria rather than any single one. Caution should be used when dimensionality-reduction methods are employed, especially when only a few of top embedding dimensions are used to describe the free energy landscape.
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DOI：
10.1002/prot.340110305
发表时间：
1991-01-01
期刊：
PROTEINS-STRUCTURE FUNCTION AND GENETICS
影响因子：
--
作者：
ICHIYE, T;KARPLUS, M
通讯作者：
KARPLUS, M
影响因子：
4.4
作者：
Spiwok, Vojtech;Kralova, Blanka
通讯作者：
Kralova, Blanka
DOI：
10.1137/0109047
发表时间：
1961-01-01
期刊：
JOURNAL OF THE SOCIETY FOR INDUSTRIAL AND APPLIED MATHEMATICS
影响因子：
--
作者：
GOMORY, RE;HU, TC
通讯作者：
HU, TC
影响因子：
3.4
作者：
Yang, MF;Lei, M;Huo, SH
通讯作者：
Huo, SH
影响因子：
2.9
作者：
Yang, Mingfeng;Yordanov, Boyan;Huo, Shuanghong
通讯作者：
Huo, Shuanghong