Similarity of chemical structures

Josef Gut jgut at
Sat Nov 6 10:10:14 EST 1999


I am looking for molecular modeling software packages that can compare
small chemical structures (such as drugs and or their
metabolites/reactive intermediates) against each other and return
something like "similarity" indices for several parameters: overall 3D
structure of the molecules (energy-minimalized conformations thereof,
electrochemical surface potentials, partial charge distributions and
their coordinates on the surface of the molecules, etc. Also, what are
the best tools to dock such molecules to proteins (receptors, substrate
binding sites, etc)?

Any any advice is highly appreciated. We are starting a programm where
we try to identify small molecules with sufficient overall structural
similarity to follow similar pathways of metabolism and eventually
producing similar adverse effects. Thanks for your help.

Joseph Gut, Ph.D.

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