[modeller_usage] Re: model different regions of a protein

[Joel Subach <mjsubach AT alumni.ncsu.edu>]

Hi Javier your welcome and thank you for your email:).

1. Did you try Alphafold?

You have one template, try and find a second template and then model.

Feel free to inquire further if needed:).

Best,
Joel 

On Wed, Sep 11, 2024 at 1:25 AM José Xavier <jxln_karate AT yahoo.com.br>
wrote:

> Dear Joel,
> Thank you for your help
>
> It's a protein with 415 amino acids and 95 are missing
>
>
>
> Em terça-feira, 10 de setembro de 2024 às 04:55:25 BRT, Joel Subach <
> mjsubach AT alumni.ncsu.edu> escreveu:
>
>
> Hi Jose, thank you for your inquiry and I can assist you in greater detail
> if I know how many residues in total you peptide/protein is, thanks:)
>
> On Tue, Sep 10, 2024 at 9:14 AM Modeller Caretaker via modeller_usage <
> modeller_usage@listsrv.ucsf.edu> wrote:
>
> On 9/9/24 4:52 PM, José Xavier via modeller_usage wrote:
> > I'm new here.. so sorry if this is an already answered question.
> >
> > I want to model a protein but the better template doesn't show ~50
> > aminoácids in its sequence. Is it possible to model the protein based on
> > this template and only the region of ~50 residues based on another
> > template?
>
> Yes, this is certainly possible with a suitable alignment; see the FAQ:
> https://salilab.org/modeller/FAQ.html#1
>
>         Ben Webb, Modeller Caretaker
> --
> modeller-care@ucsf.edu             https://salilab.org/modeller/
> Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage
>
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> modeller_usage mailing list
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>
>

Hi Javier your welcome and thank you for your email:).

1. Did you try Alphafold?

You have one template, try and find a second template and then model.

Feel free to inquire further if needed:).

Best,

Joel ð???

On Wed, Sep 11, 2024 at 1:25�AM José Xavier <jxln_karate AT yahoo.com.br> wrote:

Dear Joel, 

Thank you for your help 

It's a protein with 415 amino acids and 95 are missing

Em terça-feira, 10 de setembro de 2024 às 04:55:25 BRT, Joel Subach <mjsubach AT alumni.ncsu.edu> escreveu:

Hi Jose, thank you for your inquiry and I can assist you in greater detail if I know how many residues in total you peptide/protein is, thanks:)

On Tue, Sep 10, 2024 at 9:14â?¯AM Modeller Caretaker via modeller_usage <modeller_usage@listsrv.ucsf.edu> wrote:

On 9/9/24 4:52 PM, José Xavier via modeller_usage wrote:
> I'm new here.. so sorry if this is an already answered question.
>
> I want to model a protein but the better template doesn't show ~50
> aminoácids in its sequence. Is it possible to model the protein based on
> this template and only the region of ~50 residues based on another
> template?

Yes, this is certainly possible with a suitable alignment; see the FAQ:
https://salilab.org/modeller/FAQ.html#1

        Ben Webb, Modeller Caretaker
--
modeller-care@ucsf.edu             https://salilab.org/modeller/
Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

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