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--/------------* >P1;B structureX:B -------------/--BBBBB--* >P1;AB sequence:AB --AAAAA--/--BBBBB--*
Cheers, Han
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
participants (2)
-
Han Choe -
Modeller Caretaker