hello.... I modeled a protein using 2 templates in Modeller9...1-312 residues w.r.t one protein and the next 65 resdiues w.r.t another protein....The template selection is done carefully and both the templates share a good homology with my query sequnce.... But, i have got prolines in helix which i doubt about its existence.....Its a pretty long helix in which 3 prolines are present and 2 of them are in the middle of long helix.....There is an immediate loop following this and then another helix having 2 Prolines....
Can anybody suggsest how modeler came up with such a model having Prolines in helix?? Is it valid ?? how stable is it?? has anybody encountered with the same Proline issue with any other protein?
Please post in your views......
---------- Forwarded message ---------- From: Raghu Bhagavat bioraghu.iisc@gmail.com Date: Mon, Nov 9, 2009 at 10:53 PM Subject: More than one Proline in helix! To: modeller_usage@salilab.org
hello.... I modeled a protein using 2 templates in Modeller9...1-312 residues w.r.t one protein and the next 65 resdiues w.r.t another protein....The template selection is done carefully and both the templates share a good homology with my query sequnce.... But, i have got prolines in helix which i doubt about its existence.....Its a pretty long helix in which 3 prolines are present and 2 of them are in the middle of long helix.....There is an immediate loop following this and then another helix having 2 Prolines....
Can anybody suggsest how modeler came up with such a model having Prolines in helix?? Is it valid ?? how stable is it?? has anybody encountered with the same Proline issue with any other protein?
Please post in your views......
participants (1)
-
Raghu Bhagavat