6. Searching Relibase entries for stacking interactions
2D/3D menu. Sketch a query with the MolEd for
searching interactions between two aromatic rings:
In this query, the left aromatic ring is defined as the ligand, the right one is the
protein. Three distances in the given order are defined, all of them having the same
distance limitations (e.g. 3.5-4.0 �). With this query, one obtains 33 hits. The results page
of the search looks like this:
Results are loaded into a second browser window and one of the RasMol window is updated with
the current hit.
The distance constraints have to be restricted to a maximum distance (e.g. 6 �) in order to
get reasonable hits. The aromatic rings are forced to adopt nearly stacking positions when
defining three distances with small limitations.
Alternatively, you may also search by defining angles between two aromatic rings in the
MolEd menu.
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