What is the meaning of propensity score of amino acid? How is it calculated?
(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)


As a simplified response: Propensity score is used to predict protein secondary structure. It is derived from looking at the aa residue of the accessible surface of the protein and also the interface which enables interactions between other proteins.

The equation is as follows:

Propensity= [probability of the residue in the interface / probability of the residue on the surface]


prob of the residue in the interface = [number of amino acids in the interface / total number of amino acids of any type of interface]


prob of the residue on the surface = [number of surface amino acids / total number of surface amino acids]

Check out this PLOS paper for an example. PLoS One. 2014; 9(5): e97158.

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