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Re: [modeller_usage] DOPE score for multi chain protein
- To: Omar Piña <pibe05 AT gmail.com>
- Subject: Re: [modeller_usage] DOPE score for multi chain protein
- From: Modeller Caretaker <modeller-care@ucsf.edu>
- Date: Tue, 28 Sep 2010 17:24:35 -0700
- Cc: modeller_usage <modeller_usage@listsrv.ucsf.edu>
On 9/28/10 9:39 AM, Omar Piña wrote:
I am modelling a tetrameric protein (ion channel). I want to evaluate
the models, but I have read that the DOPE assesment is not good for
multi chain proteins
(http://www.salilab.org/modeller/9v6/manual/node242.html).
That's not correct - we simply have no benchmark data to prove whether
it is good or bad. It has only been thoroughly tested on single chains.
It *appears* to function rather well on multichain models, however.
Then, how is
the best way to evaluate them? Each chain should be evaluated
independently? Should I take only the best molpdf score?
You certainly should not use the molpdf score - the Modeller scoring
function does a great job for optimization, but it is not designed to
discriminate good models from bad models at assessment time.
Ben Webb, Modeller Caretaker
--
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