Percentage of Residues in Ramachandran Plot regions versus time of trajectory

From: Aditya Ranganathan (aditya.sia_at_gmail.com)
Date: Sun Jan 27 2013 - 22:45:13 CST

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Hello All,

I`m working in the area of protein aggregation and trying to use MD
simulations to study the secondary structural progression during
aggregation. However, I have a couple of questions. Is it possible to find
out the percentage of residues falling in the alpha helical and beta sheet
regions of the Ramachandran Plot versus time. Is there a script to do the
same over the timeframe of the simulation. Also, would STRIDE secondary
structural prediction results be drastically different from the
Ramachandran plot residue assignment. I`m a novice at writing scripts. If
there is an analysis script that does the same, it would be greatly
appreciated.

Thanks and Regards

Srivastav Ranganathan
Research Scholar
IIT Bombay

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