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[读书笔记]Plos One 上一篇突变的文章分析模式学习(简)

标题:Molecular Dynamics Analysis Reveals Structural Insights into Mechanism of Nicotine N -Demethylation Catalyzed by Tobacco Cytochrome P450 Mono-Oxygenase

杂志:Plos One

年份: 2011

影响因子:3.24

文章下载参考文献pone

方法:

1.结构准备:

建模 SWISS-MODEL ,评价 TM-score

分子对接:AUTODOCK

分子动力学:

GROMACS 4.5.3

力场:GROMOS96 53a6 force field

小分子力场:Dundee PRODRG Server

MD:30ns

2.分析:

RMSD, RMSF, Helix, and Channel analysis

RMSDs 骨架原子

C-alpha RMSFs

g_helix program 观察突变螺旋卷曲 Specifically, the helical rise per residue is plotted as the difference in Z-coordinate between Ca atoms

通道:CAVER

主成分分析和协方差分析:

PCA(Principal component analysis)分析:脚本

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Licensed under CC BY-NC-SA 4.0