Hello , i want to design a chimeric protein by fusion of subdomains of two known proteins. Do you know how should write the relevant scripts? And how to do the alignment? Should i use the multi template approach and use the two proteins as a template? Thank you! Dafni
Hi I would try multiple and a single template approach, thanks:)
On Wed, Mar 15, 2023 at 1:49 PM dafnikarr--- via modeller_usage < modeller_usage@salilab.org> wrote:
> Hello , > i want to design a chimeric protein by fusion of subdomains of two known > proteins. Do you know how should write the relevant scripts? And how to do > the alignment? Should i use the multi template approach and use the two > proteins as a template? > Thank you! > Dafni > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > https://salilab.org/mm/postorius/lists/modeller_usage.salilab.org/ >
On 3/15/23 10:49 AM, dafnikarr--- via modeller_usage wrote: > i want to design a chimeric protein by fusion of subdomains > of two known proteins. Do you know how should write the relevant > scripts? And how to do the alignment? Should i use the multi template > approach and use the two proteins as a template?
Yes, the normal way to do this would be to align your sequence with that of both templates. See https://salilab.org/modeller/FAQ.html#1
Nothing special is required in the script. The "simple" script at https://salilab.org/modeller/10.4/manual/node16.html would suffice, although you would need to list both templates in "knowns", of course.
Ben Webb, Modeller Caretaker
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dafnikarr＠gmail.com -
Joel Subach -
Modeller Caretaker