Subject: [modeller_usage] modeller model and modbase model
From: hori koshii <>
Date: Sun, 7 Jan 2007 19:27:53 -0800 (PST)
Hi all,
Has anyone come across with the models on MODBASE? How does that compare to our own models built by using "MODELLER"? (I know they are both using MODELLER, but the protein I am working on, have very different "insertion" loops from my results and modbase's)
I have been trying to build a protein model using MODELLER8, but recently come across with one already available on the MODBASE. I think there is actually only one good template (over 30%) for my target. I used MODELLER 8 to build 1000 models and pick out the ones with lower DOPE scores. The loop conformations in my model and the one on MODBASE are quite different. I am curious espeically about the loop insertions.
So, I am wondering how come they are very different? Could anyone from this forum give me any comment about this please?
Thank you
:)
Sincerely yours,
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