Dear All,
I want to start by saying that I am a rookie in secondary structure prediction and have very limited knowledge of bioinformatics.Nevertheless I tried using this server to predict the secondary structure of a peptide extrapolated from a known protein structure and changed in 2 residues. The first time I used the server, 4 months ago, I observed a huge loss in the alpha helical content (job id S120152) after this changes which correlated withe the correspondent CD spectrum.
Now by re-using the server the result I observe are completely different and the first 5 models, instead of being again more strand-like, result now all alpha-helical (job id S132282).
Did something critically changed in the algorithm or the procedure in the last 4 months?
let me know please I would like to understand such a discrepancy.
Thanks,
Gio'