Itasser: How To Decrease The Number Of Residues In The Disallowed Region ?

Question

[Rhema Susan]

I modeled a protein using online iTASSER. Now the problem is that almost 3.8% (40 residues)of the residues are in the disallowed region. I am not able to proceed further with my study because of this fact. Can anybody kindly suggest anything that can be done. Or should I just abandon the project????????? HELP plz

Answer 1

[Pals]

If your protein has homologous structures, why don't you go for homology modeling using MODELLER or SWISS-MODEL?

Okay, you come up with a model predicted by iTASSER. But why are you worried with the stereochemical quality of your protein? It just tells which residues in your model are stereochemically incorrect and it won't have marked effect if you know what you are doing with your protein. I would suggest you to pick which residues are in the disallowed regions and see if they are involved in one of the objectives of your project. Even if they are involved, interpret them carefully. Prediction is just the representation of the residues in 3-dimension based on already available experimental structures.

I do not think you should abandon your project. This small problem might help you explore more and understand more.