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<title>Generating Structures</title>
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<h2>
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<a name="Generating_Structures"></a>Generating Structures</h2>
Three-dimensional structures are generated for a mapping by:<br>
<ol>
<li>Creating an initial set of coordinates by embedding the updated
bounds matrix for each mapping [<a href="References.htm#Crippen1981">Crippen1981</a>]</li>
<li>Cleaning up the embedded structures using the Universal Force
Field (UFF).[<a href="References.htm#Rappe1992">Rappe1992</a>, <a
href="References.htm#Casewit1992">Casewit1992</a>] The
optimization is done with constraints to ensure that the final
structure still satisfies the pharmacophore.</li>
<li>Aligning the cleaned conformation to the reference pharmacophore.[<a
href="References.htm#Heisterberg1990">Heisterberg1990</a>]</li>
</ol>
Whenever possible, multiple aligned conformations are generated for
each mapping. This provides the user with an overview of the ways in
which the probe molecule can satisfy the pharmacophore.<><br>
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