Fwd: Re: model_refinement

[Modeller Caretaker <modeller-care@ucsf.edu>]

Forwarding to list.

From: Denis Volkov <D.Volkov AT artcustoms.ru>
Subject: Fwd: Re: model_refinement

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Hi, Oliver!
First of all thank you for your help!
I'll try to run Procheck on every template.
As to alignment...automatic alignment produced by Modeller and
ClustalW didn't satisfied me. The problem is that I'll try to model
unknown retroviral aspartic protease and all enzymes of this class
share a little similarity. So I used manually adjusted alignment based
on knowledge of conserved regions of this class.
No, I didn't used any restrains during all MD steps. I thought that
this is a little bit unnatural to fix one region and don't other. But
now I think that this may be a clue.
But I have another question:
If I've got so little similarity can I used a data of predicted
secondary structure(I know that Modeller can do it)? Will it improve a
quality of a model?

Thanks in advance

Denis Volkov
Enzyme Laboratory,IBCH RAS


-- 
Best regards,
 Denis                            mailto:themelon AT yandex.ru
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