Question: How to calculate the Secondary Structure similarity score between a sequence and a protein template?
gravatar for jafarzadeh91
5.0 years ago by
Iran, Islamic Republic Of
jafarzadeh910 wrote:


I am reading the paper "Fold Recognition by Predicted Alignment Accuracy" . In this paper the author first align the the input sequence with the sequence of a template protein.

Then in order to define an structural similarity between the sequence and that protein template, first predict the secondary structure for the sequence with a tool such as PSIPRED. PSIPRED assign three values to each residue (call it I) of the input sequence: Alpha_Helix(I), Beta_Sheet(I), Loop(I). We can see this values as level of confidence for each residue I to be in Alpha Helix, Beta Sheet or Loop region (consider their sum equal to one).

The contribution of paper is that for an aligned pair of residues for example residue J from the sequence and residue K from the template the algorithm define a structural similarity measure between this pair as below:

(remember that we calculated J's confidence for being in each region before with PSIPRED and also we know K's region because it is a residue from the template protein that We know everything about that.)

if K be in alpha-helix region of template


if K be in beta-sheet region of template



What I can't understand is why We reduce the loop(J) from its alpha_helix(J) or beta_sheet(J)?I think It should has a biological background but I don't know what.What I think to be true is :

if K be in alpha-helix region of template


if K be in beta-sheet region of template


ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by jafarzadeh910
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1768 users visited in the last hour