Hi Modeller users,
I have an interesting case where I have two known structures of related proteins A and B.
A is in the inactive conformation while B is in the active conformation.
Is it possible to use modeller to predict the active conformation of A using structure B as the template?
Further, despite being in different conformations, only a handful of residues are important for this conformational change (the rest remain stable and are distal from the active site).
Is it possible to hold the correct parts of protein A in place and only perform modelling on residues within the active site (taken from protein B as template)?
Best, Parker
On 9/30/15 11:54 AM, Parker de Waal wrote: > Is it possible to use modeller to predict the active conformation of A > using structure B as the template?
Sure, just do regular modeling using the sequence of A as your target and B as your template.
> Is it possible to hold the correct parts of protein A in place and only > perform modelling on residues within the active site (taken from protein > B as template)?
Certainly - just use your structure of A as the initial model: http://salilab.org/modeller/9.15/manual/node27.html
Then override select_atoms() to only select the active site: http://salilab.org/modeller/9.15/manual/node23.html
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
Parker de Waal