Question: Identifying Altered Secondary Structure From Alanine Scan?
gravatar for leonardo
8.1 years ago by
leonardo40 wrote:

Hi all,

I have used PSI-Pred to generate secondary structure predictions of each scanned alanine mutation. How do I compile all this data to look for significant deviations from the wild-type protein?

My approach was to use a sliding window (say 5 amino acids wide) and take a weighted average with respect to the centre amino acid. From this, I wasn't sure how to proceed. Maybe I could take all the averages from matching window positions and use the average to run a t-test against the wild-type.

Can you impart some wisdom?

prediction protein structure • 1.6k views
ADD COMMENTlink modified 4.1 years ago by Biostar ♦♦ 20 • written 8.1 years ago by leonardo40
gravatar for João Rodrigues
8.1 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:

I would do what you did. Align each prediction to the wild type and see where the secondary structures are more conserved throughout the scans. I would also look at regular conservation and see where you have the most conserved residues and pay more attention to those regions.

Do you have structures or can you build a model for the protein? That would be much more reliable (then again, depends on the model).

ADD COMMENTlink written 8.1 years ago by João Rodrigues2.5k

I can look at conserved residues to see if these regions are more affected than non-conserved domains. There are no crystal structures yet. Is there a more objective or statistical way to compare differences?

ADD REPLYlink written 8.1 years ago by leonardo40
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