Dear
all,
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--/------------*
-------------/--BBBBB--*
>P1;AB
sequence:AB
--AAAAA--/--BBBBB--*
Cheers,
Han