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
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?
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*From: *Modeller Caretaker modeller-care@salilab.org *Sent: *Monday, October 26, 2020 10:56 PM *To: *Sruthi Sudhakar sruthisnambiar0412@gmail.com; modeller_usage@salilab.org *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
participants (3)
-
Modeller Caretaker -
SRUTHI NAMBIAR -
Sruthi Sudhakar