Re: [modeller_usage] Conformational Modelling

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