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If a binding pocket is not known in advance, use icmPocketFinder or icmCavityFinder (for closed pockets). The protein needs to be converted to an ICM object in order to use icmPocketFinder.
icmPocketFinder can be accessed by
NOTE: A button for icmPocketFinder can be found on the Setup Receptor option in the docking menu. It performs the same function as Tools/3D Predict/icmPocketFinder |
The results from icmPocketFinder will be displayed in a table.
To view the pocket in the graphical display:
The results from icmPocketFinder are also plotted graphically (Area vs Volume). A blue square highlights potential drug binding pockets based on typical area and volume values - this is only a guide on what constitutes a pocket likely to be involved in ligand binding. Selections can also be made from the plot by clicking and dragging around a point in the graph.
To identify ligand binding pockets which are completely enclosed in the receptor:
A similar output to that generated by ICMPocketFinder will be displayed. This output includes a plot and a table. By clicking on the table or plot graphical selections can be made.
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