Dear Modeller users, 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? Thank you for your help Xavier
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
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@salilab.org> 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@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mm/postorius/lists/modeller_usage.salilab.org/
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@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@salilab.org 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
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@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@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@salilab.org> 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@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mm/postorius/lists/modeller_usage.salilab.org/ > >
Dear Ben, Thank you
I'll read it.
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Joel Subach -
José Xavier -
Modeller Caretaker