Studying fluctuations in proteins from Molecular Dynamics trajectories
View this post on Hive: Studying fluctuations in proteins from Molecular Dynamics trajectories
View this post on Hive: Studying fluctuations in proteins from Molecular Dynamics trajectories
Finally, someone explained RMSD. I have been wondering about it since my college days. Great post.
How dare you reduce my dimensions 😂
But But... I had asked your permission ages back :P
You forgot it seems.
Awww xD
Even cuter than my Caenorhabditis
Dexterdev, thank you for the post actually worth reading
Have you tried with other techniques for dimensionality reduction?
Welcome. <3
I have tried tSNE technique once.
For PCA... Your 1st and 2nd component took only 35 + 20% of variance, which is very low.
ICA is usually more resistant to noise. Or... Try something for sparse analysis, it might work better
I was attending a recent workshop about Free energy calculations and Enhanced sampling techniques in MD simulations. t-ICA technique seems to be a nice method. A talk which I attended there. It may be of your interest: https://drive.google.com/file/d/1IGVLyzYtDUqUBy_4LLrdTNLtOywV2fXu/view
Thanks man!
welcome :) I remembered you(and this thread) when the speaker started talking about ICA :)
Completely agreed. I mentioned this is as a caveat. This example was for illustration purpose. I have seen papers with ICA analysis.
I know, PCA is as popular as Kardashians. Nobody knows why - it simply is :D
I think because it is very simple and intuitive. Dimensionality reduction topics starts with pca
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