ADL: 1AIK structure

Radu TAMAIAN tradu at icsi.ro
Thu Sep 30 03:25:24 PDT 2010


Manny thanks for the point c!!! Those apps are also good for antibodies?

PhD. Stud. Biol. Radu TAMAIAN
FP7 Infrastructure NCP 
National Research and Development Institute for Cryogenics and Isotopic Technologies
ICIT Rm.Valcea 
Research and Development Department
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---------- Original Message -----------
From: Gavin Seddon <home at gavsed.net>
To: autodock at scripps.edu
Sent: Thu, 30 Sep 2010 10:37:38 +0100
Subject: Re: ADL: 1AIK structure

> Andreas,
> remember if you use an editor;
> a.  the rest of the mol is wrong unless you reminimise with md.  This my 
> be a good idea anyway.
> b.  One has to be careful not to 'chop' anything crucial, yes this 
> applies to a gui editor also.
> c.  the best protein editor tools are YASARA and WHATIF.  These will 
> also check your final structure.
> 
> Gav.
> 
> On 30/09/10 08:54, Kukol, Andreas wrote:
> > I am not sure about removing side chains, but the most easy way to remove parts of the protein including side chains is with a text editor, such as WordPad or Notepad++.
> >
> > Andreas
> >
> >    
> >> -----Original Message-----
> >> From: autodock-bounces at scripps.edu [mailto:autodock-bounces at scripps.edu] On
> >> Behalf Of chandra shekhar
> >> Sent: 30 September 2010 08:00
> >> To: autodock at scripps.edu
> >> Subject: Re: ADL: 1AIK structure
> >>
> >> use pymol for removing side chains
> >>
> >> On Thu, Sep 30, 2010 at 12:27 PM, Onur Alten
> >> <onuralten1983 at hotmail.com>wrote:
> >>
> >>      
> >>> Hello everyone. I have used the protein structure 1AIK for docking. I
> >>> download it as a biological unit from rscb. It contains 3 N-helix and 3
> >>> C-helix. I want to remove one of the C-helix.
> >>> How can I make it with autodock?
> >>> Many thanks
> >>> ________________________________________________
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> >>>
> >>>        
> >> ________________________________________________
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> >>      
> > ________________________________________________
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> >
> >
> 
> -- 
> Sent from XEON.
> ________________________________________________
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------- End of Original Message -------



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