[BiO BB] Small molecule databases

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Sat Jan 31 07:12:48 EST 2004

++ 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

One (available for download?) at BRENDA

You can get details of small molecules (hetero atoms) in the structures of the PDB
from PDB SUM

And the same data (in a different (cleaner?) form) can be sniffed from the MSD site

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

Looking through my googles I saw this

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
    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

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.


> 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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