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Re: [ccp4bb] homology modeling----good bond lengths, bad angles
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
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Subject: Re: Cannot running NTA to purify the protein having His-tag?
From: jmdias {- at -} SCRIPPS {- dot -} EDU
Date: 2007-02-28		Next message:
Subject: improve crystal size and quality -- membrane protein
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Date: 2007-02-28


Subject: Re: homology modeling----good bond lengths, bad angles
From: sudhaarsan {- at -} GMAIL {- dot -} COM
Date: 2007-02-28

Have you tried Modeller ?
-Sid.

On 2/28/07, anagha gupta wrote:
> Hi CCP4 community!
>
> I have constructed a homology model of a deletion variant of a protein whose
> structure has already been solved. These deletions are 3-4 amino acid in
> length and are in a loop that connects two helices. The model structures
> look good with respect to bond lengths in the aforementioned loop region but
> the bond angles (especially Phi and Psi) are very distorted. Ramachandran
> plot suggests the same and some of the amino acids flanking the loop are now
> in the disallowed region.
> I thought one way to avoid this is to delete one amino acid at a time and
> construct the model and use the previous model as the template to construct
> the next model. This is not working very well in fixing the wrong angles.
>
> I was wondering if
>
> 1) Anybody out there knows good homology modeling software. I used SWISS
> model and CPH model to create my models. I have heard about prime but right
> now am waiting to get the software .
> 2) Is there a way I can fix the angles if I perform an energy minimization
> of the model.
>
> Suggestions are appreciated.
> Thanks,
> Anagha.
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