PDB files & CHIME

A.J.Cann nna at le.ac.uk
Tue Nov 24 07:34:35 EST 1998


In article <nna-ya02408000R2311981157150001 at news>, nna at le.ac.uk (A.J.Cann)
wrote:

>I have been trying to find PDB files of several molecules for use with the
>CHIME plugin in a new online tutorial:
>http://www-micro.msb.le.ac.uk/Tutorials/dfwt/dfwt1.html
>I would like to find information for:
>sulphonamide
>p-aminobenzoic acid
>folic acid
>Can anyone tell me where to find thes files or how to construct them?

Many thanks to all those who replied. Summary of responses:

Jeffrey Atkinson <jatkin at spartan.ac.brocku.ca>
Try the Klotho database at http://www.ibc.wustl.edu/klotho/.  All
kinds of stuff here including the thing at least the folate that you are
looking for.  They don't have sulphonamide or PABA, but these can be easily
drawn with one of the structure packages such as ChemDraw or IsisDraw,
Spartan or Hyperchem.  The 2D IsisDraw is free on the net but does not have
3D capability.

John Osborn <j.c.osborn at Bradford.ac.uk>
If the crystal structures of these compounds have been published
they will almost certainly be in the Cambridge Crystallographic
Database. Since you are at a British university you are entitled to
register to use this database free of charge through the Daresbury
Chemical Database Service. For details see
http://www.dl.ac.uk/CDS/cds.html
The structure files you can download from the database will not be
in PDB format, but if you need this format you can probably convert
them using the free molecular data format conversion program called
BABEL, available from
ftp://ccl.osc.edu/pub/chemistry/software/MAC/babel/
There may also be data format conversion software available on the
Daresbury Chemical Database Service - I am not sure about this.

Kenward Vaughan<kaynjay at igalaxy.net>
Have you visited the following?
http://www.sci.ouc.bc.ca/chem//molecule/molecule.html
http://www.ibc.wustl.edu/moirai/klotho/
http://ourworld.compuserve.com/homepages/JDebord/models.htm
    (last one has some other links, too)
    and a place of links I just ran across, but don't know about currency:
http://sch-www.uia.ac.be/u/thys/chem.html

Jeremy Murray <bmbjmm at bmb.leeds.ac.uk>
I guess your first port of call is the cam cryst database
http://www.ccdc.cam.ac.uk/
and then maybe HICUP
http://alpha2.bmc.uu.se/hicup/

Lynda Ellis <lynda at email.labmed.umn.edu>
I enjoyed looking at your tutorial.  One place to look for pdb files would be
the ChemFinder Webserver, http://chemfinder.camsoft.com/
I did not find a pbd file for sulphonamide when I looked there, but
there was a link to the ChemSymphony site, where the chemical was
the molecule of the month for February 1998.
http://www.chemsymphony.com/gallery/html/sulfanil.html
If you have the SMILES string for a compound or draw it using their editor,
CORINA will produce a pdb file for you on the web (for at least the first
1000 compounds):
http://www2.ccc.uni-erlangen.de/software/corina/index.html

-- 
Dr Alan J. Cann  PhD,   Department of Microbiology & Immunology,
University of Leicester,  P.O. Box 138,  Medical Sciences Building,
University Road, Leicester LE1 9HN,  UK.



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