On 6/15/12 6:21 AM, Xiongzhuo Gao wrote:
Is there some way to rearrange (cut-and-past) the individual domains in the sequence alignment to allow PDE5 to serve for the template for those domains that have been determined, while still using the PDE2 template to thread the PDE6 linker region and to define the relationship of the two catalytic domains with each other?
One option would be to use PDE5 as a template, as you have done, but to extract a set of long-range domain-domain distance restraints from the PDE2 template. In principle Modeller could do this automatically with a carefully constructed alignment, but it would be tricky (first you'd have to reorder the domains so that you can align PDE2 with PDE5) so you might have more luck doing it manually (just add the linker region from PDE2 to your alignment). You can just measure a representative set of distances between domains in PDE2 (e.g. CA-CA distances) and then add them to your PDE5-based modeling as additional distance restraints:
http://salilab.org/modeller/9.10/manual/node27.html
Ben Webb, Modeller Caretaker
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