Ligand Binding to PXR
Overview
Binding Conformations from
the Geometry of Hydrogen Bonds Hydrogen bonds have a preferred geometry
that depends on the chemical neighborhood of the polar atoms. We model the observed
preferred geometry for hydrogen bonding by sticks and wedges. A hydrogen bond is
made if two polar atoms are close, and a donor stick is aligned with an acceptor
stick or wedge. These geometric constraints are formulated in an
optimization problem, whose solutions are ligand conformations that establish at least two
hydrogen bonds between a ligand and the binding pocket. We then check the candidate
conformations for steric hindrance using a hierarchical collision-detection algorithm and retain the valid conformations
in the
binding pocket.
References
People
Acknowledgement
This work has been partially funded by an
NSF-ITR grant.
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Maintained by David
Hsu Last Modified: Mon Dec 17 15:24:07 EST 2001
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