Dear all,
I want to model a sequence of 200 amino acid of brip1 protein in human, but unfortunately there is no template for this protein. I used ab-initio softwares (I-tasser and swiss model) but the model quality is very low. Kindly, could anyone advise me how can I model this sequence with an acceptable quality?
Thanks in advance for all helps
If you have the amino acid sequence with you, you can do it online by Phyre2. The link is...
http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index
Check whether it serves your purpose
Mrs/Miss Parvizpour,
You can use Gabedit (http://gabedit.sourceforge.net/). It is free of charge.
Thank you Keka Talukdar, I already used phyre2 but it gives a very low Confident model (Confidence : 14.4% Coverage: 6%). So, plz can anyone suggest more powerful software?
Dear Sapideh I suggest you to use the Modeller program
https://salilab.org/modeller/
In the tutorial section it is described very well how to use the program and the scripts you need are avalaible...it is a very reliable program!
Several programs are there to get your pdb......you can try Avogadro, Probuilder online software etc. These are free. Discovery Studio has also the facility, which is commercial. Others are also there.
In the current state-of-art for protein modelling no good template = no good model. It's as simply as that. Ab-initio protein modelling theories are OK for short sequencies, but not for 200 amino acids - they will give you completely random results with no possibility of evaluation their final quality.
The only viable option is to get first a xray/nmr structure of this or similar protein.
There are several online and free downloadable software's such as Modeller, Easy modeller and also validating the modeled structure softwares also available.
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