I have 900 PDBs and I would like calculate the propensity values of amino acids in different secondary structures which are got by sstruc program. Total 5 types of secondary structures are there in the 900 proteins. Among the secondary structures strand only found in 300 proteins out of 900 proteins. Now I have to calculate the propensity values of amino acids in strand. The formula is the ratio between frequency of a individual residue of our interest in strand and the frequency of same individual residue in the protein data.
Now my question comes here. As strand found in the only 300 proteins along with other secondary structures, for denominator (frequency of residue of our interest in protein data) calculation which protein data I have to consider, whether 900 protein data or 300 protein data?
Thanks in Advance
Surya
