Subject: 2D to 3D structure conversion

From: Scott William Chinn <[email-masked]>
Date: Wed, 19 Jul 95 02:18:47 PDT

I understand that programs such as CONCORD, CORINA and CHEM-X
can convert 2D structures to 3D. 

I have a number of 2D structures which I would like to 
convert to 3D and then store in a relational database.

Is this possible? What does the 3D data look like? I have heard
that CHEM-X will give you something like 400 bitwise operators, which
somehow describe the 3D stucture. Is this correct?

Any comments would be most helpful.

THANKS!
Scott

Name: Scott William Chinn
E-mail: [email-masked] (Scott William Chinn)

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From: [email-masked] (Toni Kazic)
Date: Wed, 19 Jul 1995 08:44:31 -0500

Scott,

It is certainly possible.  I have some experience with CONCORD, having used
it to convert isomeric SMILES strings to pdb files (there are more choices
of input and output formats).  The pdb files produced contain the smiles
string, the Cartesian coordinates, and a connection table, and can easily
be read by humans or other programs.  You can view several hundred at
http://ibc.wustl.edu/klotho/.  If your SMILES string doesn't specify the
stereochemistry, CONCORD will try and choose for you.  The structures it
gets usually accord pretty well with both chemical intuition and crystal
structure (see J. Chem. Info CS 33:155-163, 1993), though it does have
limitations and does sometimes produce a howler.  I have no experience with
Corina yet, but from what I hear and read its strengths are complementary
to CONCORD's weaknesses and would be a good alternative (please let's not
have a flame war).  They now have a free email server, and I'm planning to
try it out (it's been reported on this list just recently).  I have no
experience with ChemX.  The hardest part may be generating the input for
the conversion program; if you think Klotho would be of some assistance to
you please let me know.

You may be able to find coordinates for your molecules.  For example the
NCI has its files up on a gopher server, though last time I looked there
was no easy way of retrieving a specific molecule.  Try the NIH web site, I
think there is a pointer from there (sorry I am unable just now to give you
the complete address).  Data from Cambridge Crystallographic Database are
proprietary.  I know a number of software vendors sell databases of small
molecules in various forms, usually bundled with their software.

You may want to give some thought to the types of queries you wish to run:
this has a significant impact on choice of database model, organization of
the database, and representation of the data.

Good luck,

Toni Kazic
Institute for Biomedical Computing
Washington University