Molecular Modeling

Gilbert Syswerda syswerda at bbn.com
Wed Dec 5 14:46:33 EST 1990

I am looking for the results of work people have done in the area of
predicting the chemical and physical properties of molecules. What would be
ideal is a program that could compute properties of a molecule based on its
formulation. The kind of information that would be useful is
hydrophobicity/philicity, electron withdrawing/donation,
aliphatic/aromatic, flexibility/rigidity, planar/non-planar (and other
topological features), and heterocyclic/non-heterocyclic. Properties of
molecules in solution would also be very useful.

The idea here is that there are large databases of molecules with known
interactions (e.g. binding rate at a receptor site in the nervous system).
Various techniques (e.g. ID3) could be applied to these databases to
construct classification schemes, and these could then be used to predict
the properties of new molecules. For this to work, a meaningful set of
parameters (like those listed above) must exist for each molecule. These
parameters are difficult and costly to obtain experimentally; it is usually
easier to simply try the molecule to see if it has the desired effect.

The parameters are also probably difficult to compute as well, but some are
easy (e.g. molecular weight). At any rate, I would like to find out what
can be computed today and what the general state-of-the-art is in this area.

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