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

[Daan Virtual <vdava@davapc1.bioch.dundee.ac.uk>]

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Hi

Such tools are already available - people just have to use them.
For refmac there's the Sketcher and automatic topology generation
For CNS there's
- the HICup site by Gerard Kleywegt
  http://xray.bmc.uu.se/hicup/welcome.html
- the PRODRG server
  http://davapc1.bioch.dundee.ac.uk/prodrg  (also does SHELX topologies)

In addition, there is a very powerful initiative at the EBI to generate
standard topologies for and check the geometry of small molecules in the
PDB - http://www.ebi.ac.uk/msd/index.html and links therein.

In my opinion it is impossible to get C-C distances of 2 Angstrom or
non-planar aromatic rings (there many of those in the PDB) with any of
these tool.

cheers

Daan


On Fri, 15 Nov 2002, Otterbein, Ludovic wrote:

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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..
>
>
> ***  For details on how to be removed from this list visit the  ***
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>
>
>
> -------- 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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##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava@davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

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