[Dock-fans] Dock-fans Digest, Vol 76, Issue 2

Zhong, Shijun szhong at rx.umaryland.edu
Thu Sep 9 06:57:41 PDT 2010


Hi,
 
In principle, it is not necessary to have the complete structure for docking because the calculation is mostly based on pairwise interactions. Therefore, only residues within a distance, say 10 angstroms, from the binding site (center or edge? think it!) are considered. In crystal structure, some residues are truncated because they are not important, or very flexible and far away from the binding site. Anyway, it is better to view the structure and check if any residue is missing near the binding site, especially the residues within 5 angstroms. Hope this is helpful.
 
Shijun Zhong
sjzhong at gmail.com
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Subject: Dock-fans Digest, Vol 76, Issue 2

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Today's Topics:

   1. Re: Sequence and Structure Length doesn't Match (Scott Brozell)


----------------------------------------------------------------------

Message: 1
Date: Wed, 8 Sep 2010 13:01:46 -0400
From: Scott Brozell <sbrozell at rci.rutgers.edu>
Subject: Re: [Dock-fans] Sequence and Structure Length doesn't Match
To: Mohd Afiq Hazlami <afikolami at gmail.com>
Cc: dock-fans at docking.org
Message-ID: <20100908170146.GI19135 at casegroup.rutgers.edu>
Content-Type: text/plain; charset=us-ascii

Hi,

On Tue, Sep 07, 2010 at 09:44:21AM +0800, Mohd Afiq Hazlami wrote:
> Hi, I have a question. I got a crystallized protein structure from PDB
> that's 170 AA in length. But the complete sequence length of the protein I
> got from UniProt shows that the length is 529 AA. Is it okay to go through
> with the docking procedures with this protein? Thanks.

I've never used UniProt, but there are a lot of possible sources for
the length discrepancy.  You should scrutinize the pdb entry,
visualize it, read the refs, etc.
Some obvious possibilities are alternate or unresolved residues,
domains, etc.  Depending on the purpose of the docking these could be
fatal problems...

good luck,
Scott



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