[BiO BB] Small molecule databases

[Dan Bolser]

++ Dr.Nagasuma Chandra--
>
> Hi
>
>   We are trying to get a database of the three-dimensional structures of
> small molecules that are already synthesized and available (for eg., in
> SIGMA/ALDRICH etc), as a supplement to the CSD database, which we have.  Any help
> regarding the websites containing some information and
> distributors dealing with this will be greatly appreciated.

There is a (or *the*?) ligand database at KEGG
http://www.genome.ad.jp/kegg/kegg2.html

One (available for download?) at BRENDA
http://www.brenda.uni-koeln.de/

You can get details of small molecules (hetero atoms) in the structures of the PDB
from PDB SUM
http://www.biochem.ucl.ac.uk/bsm/pdbsum/ligands/

And the same data (in a different (cleaner?) form) can be sniffed from the MSD site
http://www.ebi.ac.uk/msd-srv/chempdb/cgi-bin/cgi.pl

However, I always thought CSD was most comprehensive (but it was not free!).

Looking through my googles I saw this
http://www.netsci.org/Resources/Web/small.html


I once did a small project with Jim Austin at the University of York, he was working
on ligand matching using novel hardware (at that time simulated in software).

Performance Evaluation of a Fast Chemical Matching Method using Distributed Neural
Relaxation,
    A.Turner and J. Austin,
    Proceedings of: Fourth International Conference on Knowledge-Based Intelligent
Engineering Systems and Allied Technologies (KES'2000), Vol. 1, pp.201-204, Sept
2000.


Which is in effect holographic memory, which I always thought was cool. - Nothing to
do with my project with him though!

You can find his research pages on the university of York (UK) website.

Anybody know of a 'structural classification of ligands' (SCOL) data base? I think
this would be a great project.

Ta,
Dan.

> Cheers
> ***********************************************
>    Dr. Nagasuma Chandra
>    Bioinformatics centre
>    Indian Institute of Science
>    Bangalore 560 012
>    Tel: +91-80-3092469 or 3601409
>    Fax: +91-80-3600551
>    e-mail: nchandra at physics.iisc.ernet.in
> ***********************************************
>
>
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