Re: [modeller_usage] Query regarding the modelling of a particular set of residues in a protein

[Modeller Caretaker <modeller-care@ucsf.edu>]

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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