[modeller_usage] Re: Design of a chmieric protein from two known structures

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