Re: [modeller_usage] Conformational Modelling

[Modeller Caretaker <modeller-care@ucsf.edu>]

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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