Three-Dimensional Molecular Structure Tables - Design and Use of Relational Databases in Chemistry - page 136

associated with it, as well as an array of coordinates. If more information
is needed for conformations, additional columns can be added. Enough
information must be stored in the conformation table to allow a meaning-
ful selection. This might include a method , date , or any other identifying
information.
In order to select conformations using the vla4 schema described
earlier, the following SQL might be used.
Select structure.cansmiles, structure.name,
conformation.energy, conformation.coords
From vla4.structure Join vla4.conformation Using (id)
Where name = 'BMCL-1051-14';
This applies the same technique used throughout this topic to join two
related tables to select data from either table. This statement will select all
the conformations for the named compound. Of course, further selection
criteria could be added as desired to select the required conformation(s).
11.9 Other Representations of Three-Dimensional
Molecular Structure
While atomic coordinates form the fundamental structure of a molecule,
many methods prefer to represent a three-dimensional structure as a sur-
face or a shape. Of course, these are ultimately computed from the atomic
coordinates and perhaps atomic partial charges. It may be possible to rep-
resent these molecular surfaces or shapes as an array of three-dimensional
coordinates. These could be stored as a column in the database analo-
gous to the array of atomic coordinates. It might be necessary to create
another data type, perhaps a composite data type, to store molecular sur-
faces or shapes. Once these representations are stored, they can be used
in new SQL functions to assist in searching based on molecular surface
or shape.
References
1. O'Donnell, T.J., Rao, S.N., Koehler, K., Martin, Y.C., and Eccles, B. 1990. A
general approach for atom-type assignment and the interconversion of
molecular structure files. J. Comp. Chem . 12(2):209-214.
2. OpenBabel. http://openbabel.sourceforge.net/ (accessed April 18, 2008).
3. QSAR World. http://www.qsarworld.com/ (accessed April 18, 2008).
4. Porter, J.R., Archibald, S.C., Brown, J.A. et. al. 2003. Dehydrophenylalanine
derivatives as VLA-4 integrin antagonists. Bioorg. Med. Chem. Lett . 13(5):
805-808.
5. VLA4 dataset. http://www.qsarworld.com/qsar-datasets-porter.php
(accessed April 18, 2008).