Protein Structure Prediction

Question

[Pratheep]

My protein of interest contain 3500 a.a residues, its possible to predicting the structure through Homology modeling and / or any other tolls are there for prediction. Thank you in advance for your help

Answer 1

[AsoInfo]

You can predict the structure on the basis of Homology Modelling as well as on the basis of ab initio structure prediction (It depends on the availability of template). For homology modelling, you need to have a suitable template for your target protein. Your protein size is considerably big, so there is a possibility that you could find a protein template that can only show homology in a specific part of your protein. The rest of the protein structure will not be defined.

MODELLER is the preferred software for Homology Modelling. I have used I-TASSER (linux version) for the sequence-based structure prediction. There are many online web servers are also present like Phyre2, I-TASSER server, LOMETS, QUARK and you can use any of them for your structure prediction.

Answer 2

[João Rodrigues]

3500 residues? My opinion, divide it into domains and use MODELLER/I-Tasser accordingly. PHYRE and/or HHpred might also help sometimes. Don't even try to input the entire thing in any server as they won't either accept it because of the length, or produce a bad model because of mismatches.

[tommy.carstensen]

If your protein is 3500aa, then it is most likely a multi domain protein. As already suggested I would split it into relevant domains.