Re: [modeller_usage] how to build the loop of protein model using modeller

On 4/29/13 8:25 PM, aixintiankong wrote: > i don't know how to build a model that the protein, NAD+ and ligand > coexsit and the loop of protein is disordered.

One way to do this would be to align your model sequence with the first template (loop is helix) for the entire sequence except the loop, and the second template (loop is disordered) for the loop: http://salilab.org/modeller/9.11/FAQ.html#1

Another way would be to just use the first template, and just unalign the loop so Modeller builds it without template information: http://salilab.org/modeller/9.11/FAQ.html#2

Ben Webb, Modeller Caretaker