Re: [modeller_usage] modeller model and modbase model
To: hori koshii <>
Subject: Re: [modeller_usage] modeller model and modbase model
From: Eswar Narayanan <>
Date: Sun, 7 Jan 2007 21:38:43 -0800
Cc:
The quality of homology models, especially ones with low sequence
identity, are dependent on the quality of the alignment used. The
models in MODBASE are calculated using alignments from PSI-Blast or
IMPALA. Due to the heavy computational requirements of calculating
models on a large-scale, as is the case with MODBASE, only one model
is calculated per alignment.
Now, assuming that the alignment in MODBASE is very similar to yours,
the best models you picked out of the 1000 are probably better than
what is available in MODBASE.
Eswar.
On Jan 7, 2007, at 7:27 PM, hori koshii wrote:
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,
__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com
_______________________________________________
modeller_usage mailing list
https://salilab.org/mailman/listinfo/modeller_usage