Protein Or Peptide Modelling

Question

[ivpz]

Hi, I've tried to model the tertiary structure of a 191 aa protein using various web servers (swiss model, modweb, i-Tasser, ect) but they all gave me different results because of low similarity to known templates. However, since I'm only interested the first 24 aa of the N-terminus, I'm wondering if I can simply model this short peptide and say something about it.

Thank you.

Answer 1

[João Rodrigues]

If those 24 aminoacids of the protein have similarity to something, yes, otherwise, you can try to say something but it's as valid as drawing a random coil.. Try running secondary structure predictors, running homology with HHPred for example and seeing if any homologue includes that region, etc. Don't go blindly for the 3D model, analyse the alignment first.