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RE: [ccp4bb]: [Fwd: pdb-l: Bad geometry] - for us to discuss too..



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Hi,

This is a very interesting point that you have raised. From my point of view
geometry ligand definition problems could probably be solved if we could
have some people to develop powerful and efficient tools to create small
molecule dictionaries.

Cheers


Ludovic


Ludovic Otterbein, PhD
AstraZeneca, Alderley Park
Macclesfield, UK, SK10 4TG
' : + 00 44 1 625 51 0848


-----Original Message-----
From: Eleanor J. Dodson [mailto:ccp4@ysbl.york.ac.uk]
Sent: 15 November 2002 09:33
To: ccp4bb@dl.ac.uk
Subject: [ccp4bb]: [Fwd: pdb-l: Bad geometry] - for us to discuss too..


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***          CCP4 home page http://www.ccp4.ac.uk         ***



-------- Original Message --------
Subject: pdb-l: Bad geometry
Date: Fri, 15 Nov 2002 09:26:21 +1000
From: Joel Tyndall <j.tyndall@mailbox.uq.edu.au>
To: pdb-l@sdsc.edu

Hi folks,

I wish to raise this point mainly for discussion.

I recently came across several papers and the corresponding crystal 
structures in the pdb. These were of inhibitor enzyme complexes. 
Whilst looking at these structures I noticed that the geometry of the 
inhibitors was very bad. In my opinion bad enough to break the rules 
of what is known about organic chemistry and molecular geometry eg 
C-C bond distance up to 2.0 angstrom.

Here is the problem. I have contacted the author I hope in a 
diplomatic manner and received a reply stating that they were 
interested in continuing the discussion. I have since heard nothing 
after my follow up. I have subsequently contacted the people at the 
pdb and they have said there is nothing they can do as the structures 
have been released ( but not completely checked).  It is not the 
fault of the journals which published the articles as they were not 
provided with the coordinates.

At this point I still feel that there could be a better process but I 
do not know what would be appropriate to avoid further release of 
"bad" crystallographic information. Whilst protein structure is 
checked using procheck etc, the small molecules are not. Issues can 
arise with conflicts of interest for reviewers when provided with 
coordinates prior to publication.

I am at a loss as to the next step to be taken. Any comments would be 
greatly accepted. I am reluctant to release any details of the 
structures to try and maintain some decorum...at least at this stage.

Many thanks

Joel
-- 
________________________________________
Joel Tyndall, PhD
Research Officer

http://www.imb.uq.edu.au
Institute for Molecular Bioscience
incorporating
Centre for Drug Design and Development
Centre for Cellular and Molecular Biology
The University of Queensland
Brisbane
Australia 4072

Tel:  +61 7 3365 1271
Fax: +61 7 3365 1990

email: J.Tyndall@mailbox.uq.edu.au

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