Hello,
I have a WT protein which I got the structure from the PDB. I have a mutation happing on a single point amino acid. I want to see how this mutation influence on specific domian. I want to know if I am doing it right or not
1- I installed modeller on a Mac (high Sierra) 2- I search for the sequence on Uniprot and then I arange it as
>P1;myseq sequence:myseq:::::::0.00: 0.00
with a * at the end of sequence and save it as myfile.ali
what step should I follow and or which script should I use ?
Thanks, Mohammad
On 7/20/18 8:59 AM, Mohammad Goodarzi wrote: > I have a WT protein which I got the structure from the PDB. > I have a mutation happing on a single point amino acid. > I want to see how this mutation influence on specific domian. I want to > know if I am doing it right or not ... > what step should I follow and or which script should I use ?
This is simple comparative modeling where your target sequence is identical to your template sequence except for one residue. A script similar to that at https://salilab.org/modeller/9.20/manual/node16.html should work just fine. Alternatively, you can try the mutate model script at https://salilab.org/modeller/wiki/Mutate%20model
Ben Webb, Modeller Caretaker
Hi,
I followed this modeling template https://salilab.org/modeller/tutorial/basic.html is this a correct one ? the script you showed was part of it too
Bests Mohammad
On Mon, Jul 23, 2018 at 8:25 PM Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 7/20/18 8:59 AM, Mohammad Goodarzi wrote: > > I have a WT protein which I got the structure from the PDB. > > I have a mutation happing on a single point amino acid. > > I want to see how this mutation influence on specific domian. I want to > > know if I am doing it right or not > ... > > what step should I follow and or which script should I use ? > > This is simple comparative modeling where your target sequence is > identical to your template sequence except for one residue. A script > similar to that at https://salilab.org/modeller/9.20/manual/node16.html > should work just fine. Alternatively, you can try the mutate model > script at https://salilab.org/modeller/wiki/Mutate%20model > > 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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Modeller Caretaker -
Mohammad Goodarzi