Missing Residues Modeling for an Oligomer Inquiry
Hello,
I am trying to model missing residues for a heptamer via the below Modeller link, is Modeller able to model these 12-missing residues in each of the seven exterior cytoplasmic loop-regions via a properly formatted alignment.ali file or would modeling just the missing residues for a single monomer work best for Modeller? (I would then oligomerize the complete monomer elsewhere.)
* I had read the below on the Modeller Forum that Modeller may not have the monomer interface modeling ability hence my inquiry.
*https://salilab.org/modeller/wiki/Missing_residues https://salilab.org/modeller/wiki/Missing_residues*
On 8/27/22 12:03 PM, Joel Subach via modeller_usage wrote: > I am trying to model missing residues for a heptamer via the below > Modeller link, is Modeller able to model these 12-missing residues in > each of the seven exterior cytoplasmic loop-regions via a properly > formatted alignment.ali file or would modeling just the missing residues > for a single monomer work best for Modeller?
Modeller can remodel all chains simultaneously. It may be more efficient to remodel just the monomer though, particularly if you are working with a homoheptamer and the missing loops don't interact with each other.
Ben Webb, Modeller Caretaker
Hello Ben thank you for your kind update:).
On Tue, Aug 30, 2022 at 5:45 AM Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 8/27/22 12:03 PM, Joel Subach via modeller_usage wrote: > > I am trying to model missing residues for a heptamer via the below > > Modeller link, is Modeller able to model these 12-missing residues in > > each of the seven exterior cytoplasmic loop-regions via a properly > > formatted alignment.ali file or would modeling just the missing residues > > for a single monomer work best for Modeller? > > Modeller can remodel all chains simultaneously. It may be more efficient > to remodel just the monomer though, particularly if you are working with > a homoheptamer and the missing loops don't interact with each other. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >
participants (2)
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Joel Subach -
Modeller Caretaker