Sir,
The rest of the target protein is in the form which I want (requires no modelling). So after modelling the residues 700-900, I want to join the modelled region back to the 1-699,901-1200. How can I do this? Could you please give any suggestion?
From: " target="_blank">Modeller Caretaker
Sent: Monday, October 26, 2020 10:56 PM
To: " target="_blank">Sruthi Sudhakar; " target="_blank">
Subject: Re: [modeller_usage] Query regarding the modelling of a particular set of residues in a protein
On 10/26/20 4:02 AM, Sruthi Sudhakar wrote:
> I would like to know if it is possible to model
> just this residue 700-900 with respect to my template to get it into the
> active form.
Sure, just include only the 700-900 sequence in your alignment for the
target (model) and align it with the relevant section of your template.
> If yes, should I use the whole protein template or the
> region corresponding to the one which I want to model in my target
> protein?
Whichever works best for you. You can include the whole template if you
like and just align it with gaps (-) in the target sequence in regions
where you don't want to use it in the model (i.e. residues 1-699,
901-1200). Or read only residues 700-900 from the template and align
just that with your model.
> Also after modelling this residues, How could I combine this
> back to the rest of the target protein.
If the rest of the protein is disordered, there is little point in
modeling it.
Ben Webb, Modeller Caretaker
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