Residue fluctuations analysis using PCA

[Former user]

I have read some literatures that using PCA to analysis the fluctuations of each residue. Can Bio3D do these analyses? What should I need to do? Thank you！

[guoqin feng]

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Bakan, A.; Bahar, I. The Intrinsic Dynamics of Enzymes Plays a Dominant Role in Determining the Structural Changes Induced upon Inhibitor Binding. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 14349−14354.

[Xinqiu Yao]

Hi,

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The pc$au output of Bio3D pca() function may be what you are looking for. It is a matrix with each column the normalized displacement of each atom along each PC. So, to calculate the fluctuation, just take the square and sum over PCs you want to use. Don’t forget to multiple each PC with the associated eigenvalue, pc$L, to get the correct unit.

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For example, to calculate fluctuation using PC1 and PC2:

f <- pc$au[, 1]^2*pc$L[1]+pc$au[, 2]^2*pc$L[2]
plot(f, type="l")

Please double check if this is what you want. Let me know if you have further questions.

[guoqin feng]

Thanks, Xinqiu! I think it should be like this, and I have got the analysis results. But I don’t quite understand what it means to calculate fluctuations in this way. I have seen some people use pc$au’s arithmetic sum to describe the residue fluctuations of the system, as shown in the figure below. What is the difference between the two and which way of thinking is better?

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