Subject: Re: [modeller_usage] Modelling an oligomer
From: Modeller Caretaker <>
Date: Fri, 17 Oct 2008 01:29:46 -0700
Cc: modeller list <>
Lucas Bleicher wrote:
> I want to model a heterotrimer consisting of proteins A, B and C,
> where the structure of the A:B complex is already known, and C should
> be modelled. There is a known structure of another structure made of
> proteins D, E and F, where D and E are homologous to A:B (and can be
> easily spatially superposed) and F is homologous to C.
> Do I have to work with restraints or is there a way to set a PIR file
> using the A:B and D:E:F complexes as "knowns" so that Modeller can
> assume that it must build an A:B:C complex so that A:B would be in
> the equivalent positions to D:E (but should of course be nearly
> identical to the A:B x-ray structure more than the D:E structure,
> since A:B is the real thing) and C must be modelled using F as
> template and be in the position it would occupy in the D:E:F
I can't think of an easy way to do this with a Modeller alignment.
Probably the easiest thing to do is to make a structural superposition
of your A:B and D:E:F templates, then make a new PDB file (e.g. by
simple cut and paste) containing A:B:F in their superposed orientations.
Then you can simply use this A:B:F pseudo-template to build your model.
Ben Webb, Modeller Caretaker
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage