Question: Protein Or Peptide Modelling
gravatar for ivpz
6.9 years ago by
United Kingdom
ivpz10 wrote:

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.

protein-structure • 2.4k views
ADD COMMENTlink modified 6.9 years ago by João Rodrigues2.5k • written 6.9 years ago by ivpz10
gravatar for João Rodrigues
6.9 years ago by
João Rodrigues2.5k
Stanford University, U
João Rodrigues2.5k wrote:

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.

ADD COMMENTlink written 6.9 years ago by João Rodrigues2.5k
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