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Re: [modeller_usage] combining two proteins

On Fri, Nov 19, 2004 at 11:28:15AM +0900, Han Choe wrote:
> Let's say that I have two pdb files of protein A and protein B and that
> approximate interactions of the two proteins are known. Then can I get a
> complex structure using MODELLER by restraining the distances of two or
> three interactions between A and B in the top file with the following type
> of alignment file?
>  
> >P1;A
> structureX:A
> --AAAAA--/------------*
> >P1;B
> structureX:B
> -------------/--BBBBB--*
> >P1;AB
> sequence:AB
> --AAAAA--/--BBBBB--*

Sure, something like that should work. The quality of the final model
will be very dependent on the number and type of A-B restraints you
define, however, and you may need so many restraints that the
optimization time becomes prohibitive.

	Ben Webb, Modeller Caretaker
-- 
             http://www.salilab.org/modeller/
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