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The Berkowitz group has a longstanding interest in the synthesis of unnatural phosphonates and in their use to probe active sites and glycoprotein receptor binding pockets, for example.
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Figure 8c shows an example of binding pockets for Rv3436c and mapping of the conserved residues on it.
The dataset was used to develop virtual binding pockets for accommodating HLA-II specific sHLA-II specific
The binding pockets for HT ligand binding are indicated by orange arrows.
Drug target structures are preferably molecules that contain binding pockets for known low molecular-weight compounds.
Humanized hapten-binding IgGs were designed with an accessible cysteine close to their binding pockets, for specific covalent payload attachment.
For example, a typical binding pocket for an α-helix is formed by a few adjacent subpockets that collectively form an elongated crevice that can accommodate side chains projecting out from one side of the α-helix.
A 10 Å sphere around the centre of the binding pocket was defined as binding pocket for the docking runs.
Also, a clear definition of the binding pocket for KZ7088 has been presented.
This cavity could serve as a potential binding pocket for inhibitor design.
The hydrophobic region around the adenosine creates a binding pocket for ATP.
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