Dear all,
I hope you can give me your opinion in my case.
I have a 3D structure of a wildtype protein (X-Ray) and I want to mutate one amino acid (substitution) and obtain the new structure that contains the introduced structural changes by the mutation. Also, the sequence of the protein is known.
I see an example on Modeller website for a Mutated model:
https://salilab.org/modeller/wiki/Mutate%20model
which show how to introduce a mutation and then the conformation of the mutant sidechain is optimized by conjugate gradient and refined using some MD.
Another way of doing it is to provide the PDB file and an alignment of the protein sequence and its mutant version and perform homology modelling using Modeller.
Any idea which method is preferable considering that both can be performed using Modeller to achieve the same goal here?
Thank.
Best regards.
On 11/15/19 8:56 AM, Ammar, Ammar (Stud. SCI) wrote: > Any idea which method [mutate model vs. comparative modeling] is > preferable considering that both can be performed using Modeller to > achieve the same goal here?
The mutate-model script only optimizes the coordinates of the single residue that is mutated. The regular comparative modeling script will optimize the coordinates of the entire protein. So it depends what you want to achieve here.
Mutate-model will be roughly equivalent to comparative modeling with everything but that one residue held fixed, but it will be more efficient since it doesn't bother to build the template-derived restraints.
Ben Webb, Modeller Caretaker
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Ammar, Ammar (Stud. SCI) -
Modeller Caretaker