Re: [modeller_usage] Modeling a dimer

[Modeller Caretaker <>]

On 6/7/10 4:15 PM, Konstantin A. Odynets wrote:
> my templates are a homodimer of the first domain and a monomer of the
> second domain,
> and the target protein is a homodimer. Both domains are linked by 17 aa
> flexible regions
> without templates. How could I do such task in Modeller 9.8?

You are going to have trouble with the 17aa linker regions - that's a 
little long for loop modeling. But to model the second domain, simply 
use two copies of your second template in your alignment, e.g. something 
like:

>P1;1n3l
structureX:1n3l:4:A:342:B:hstyrrs-N_2x342:homo sapiens:1.18:0.18
-AAAAAAAAAA-AAAAAA-------/-BBBBBBBBBB-BBBBBB-------*
>P1;1ntg-1
structureX:1ntg:2:A:170:A:hstyrrs-C_1x169:homo sapiens:2.21:0.251
-------------------CCCCCC*
>P1;1ntg-2
structureX:1ntg:2:A:170:A:hstyrrs-C_1x169:homo sapiens:2.21:0.251
---------------------------------------------------/--------------------------------------CCCCCC*
>P1;hstyrrs
sequence:hstyrrs:1:A:528:B:hstyrrs_2x528:homo sapiens:2.00:-1.00
AAAAAAAAAAAAAAAAAALCCCCCC/BBBBBBBBBBBBBBBBBBLCCCCCC*

	Ben Webb, Modeller Caretaker
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