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10.34 Substructure Superposition
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[ Table to Template Superposition | Rigid Substructure Superposition | Flexible Substructure Superposition ]

Available in the following product(s): ICM-Chemist | ICM-Chemist-Pro | ICM-VLS

Chemical superposition can be undertaken in the following ways.

NOTE: The substructure superposition requires topologically exact match with the template. As long as there is a large consistent scaffold then the substructure superposition is the best approach. In cases where the structures differ topologically then the APF methods should be used to superimpose moieties which have similar properties.

10.34.1 Rigid Superposition of Compounds in a Table onto a Template in The Graphical Display


Here we describe how to superimpose chemicals from an ICM Molecular Table onto a 3D template displayed in the graphical display.

  • Load the template chemical into the 3D display. It needs to be a non-ICM object. To convert an ICM object into a non-icm object: right click on the name of the object in the ICM workspace and select convert to non-ICM. You should see that the object is now labeled as a model in the ICM workspace.
  • Select the chemical template. One way to do this is to double click on the chemical name in the ICM Workspace (selected=blue in ICM Workspace and green crosses in graphical display).
  • Select the chemical(s) (row(s)) in an ICM Molecular Table.
  • Right click on the table and select Chemistry/Chemical Template Superposition and a table a data entry window as shown below will be displayed.

  • Enter the name of the template or use as_graph if you selected the template as described above.
  • The effort value (formerly 'thoroughness') represents the sampling length. The higher the value the longer the sampling takes.
  • Select whether or not you wish the rings to be sampled.
  • Click OK and the selected chemicals will be superimposed on the template in the chemical display.

10.34.2 Rigid Substructure Superposition


Here we describe how to perform a rigid-superposition of chemical structures in the graphical display:

  • Select the chemicals you wish to superimpose.One way to do this is to double click on the chemical names in the ICM Workspace whilst holding down the control button (selected=blue in ICM Workspace and green crosses in graphical display) or hold the right mouse button and drag over the chemicals in the graphical display.
  • Chemistry/Rigid Substructure Superimpose
  • A window will be displayed. Enter the name of the template structure using the ICM selection language. The ICM selection language can be found by right clicking on the molecule in the ICM Workspace - first line of right click menu.
  • Click OK

NOTE: Superimposed chemicals can be separated easily using the Arrange as grid option (Tools/Superimpose).

10.34.3 Flexible Substructure Superposition


Here we describe how to perform a flexible-superposition of chemical structures in the graphical display:

  • Select the chemicals you wish to superimpose.One way to do this is to double click on the chemical names in the ICM Workspace whilst holding down the control button (selected=blue in ICM Workspa ce and green crosses in graphical display) or hold the right mouse button and drag over the chemicals in the graphical display.
  • Chemistry/Flexible Substructure Superimpose
  • A window will be displayed. Enter the name of the template structure using the ICM selection language. The ICM selection language can be found by right clicking on the molecule in the ICM Workspace - first line of right click menu.
  • Click OK

NOTE: Superimposed chemicals can be separated easily using the Arrange as grid option (Tools/Superimpose).


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