Dear team,
How to model the missing N-terminal residues (Residue number: 1-16) from the protein structure?
My PDB structure consists of residues beginning from residues number 17. We tried modeling the structure using advanced modelling. When the missing residues were given in the loop refine step, there occurred an error stating, "The region cannot be found on the template"
Is there any way you could help us in modelling the missing residues from the N-terminal?
Thanks in advance
Aathithya D SASTRA University Thanjavur
On 10/23/20 10:31 PM, Aathithya Diaz wrote: > How to model the missing N-terminal residues (Residue number: 1-16) from > the protein structure?
This is straightforward; just add an insertion at the start of your alignment (i.e. add 16 residues to the model sequence, and 16 gaps to the template):
template ----------------aaaaaaaaaaaaaa target bbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
Note though that since Modeller has no template for this sequence, and only one end is constrained by known structure, most likely you'll get an extended chain. Since such a model is of little further use, it's usually better just to exclude these termini.
Ben Webb, Modeller Caretaker
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Aathithya Diaz -
Modeller Caretaker