Scaffold Decomposition Panel

This panel can be used to set up and run a job to decompose a set of structures into its constituent scaffolds.

To open this panel, do one of the following:

  • Click the Tasks button and browse to Structure Analysis → Scaffold Decomposition
  • Click the Tasks button and browse to Materials → Tools → More Tools → Scaffold Decomposition
  • Using
  • Features
  • Additional Resources

Using the Scaffold Decomposition Panel

The scaffold decomposition performs two tasks: detecting scaffolds in the structures, and then for each scaffold, finding the structures that contain the scaffold.

The largest scaffold is obtained by removing all side chains from any ring system in the structure. Subscaffolds are then identified by breaking all possible combinations of links between ring systems, except for fused rings.

Fused rings are not decomposed into smaller scaffolds. However, if the structure set contains a combination of fused ring systems and their subsystems (such as benzimidazoles and imidazoles), you can select Allow embedded matches to identify the subsystems of a fused ring system as scaffolds when matching scaffolds to structures, e.g. imidazoles as scaffolds in a benzimidazole.

Scaffold Decomposition Panel Features

Analyze structures from option and menu

Select this option to start a new scaffold decomposition job, and choose the source of the structures to decompose into scaffolds. You can take structures from the Project Table or a file.

Restore results from previous run option

Select this option to read the results from a previous scaffold decomposition job, and examine the results.

File name text box and Browse button

If analyzing structures from a file or restoring results from a previous run, enter the file name in the text box, or click Browse and navigate to the file.

For new scaffold decomposition jobs, the file must be a structure file in Maestro, SD, CSV, or SMILES format.

When restoring results, the file must be named jobname_scaffolds.dat, and there must be a corresponding structure file that contains the structures used in the decomposition.

Wait for results option

If this option is selected, the results of the decomposition are displayed in the Scaffold Decomposition of jobname Panel when the job finishes. If you deselect this option, you can display the results by selecting Restore results from previous run, specifying a results file, then clicking Restore.

Allow embedded matches option

Allow subsystems of a fused ring system to be matched to scaffolds when identifying structures that contain the set of scaffolds. This only applies to matching, not to detection of scaffolds. If the subsystem of a fused ring system does not exist independently in the set of structures, it is not detected as a scaffold. For example, if the structure set contains imidazoles and benzimidazoles, then the imidazole scaffold is identified in the benzimidazoles when finding the structures that contain each scaffold. However, if the structure set contains benzimidazoles but not imidazoles, imidazole is not detected as a scaffold and is therefore not identified in the benzimidazoles.

Action button

The action button at the lower left chages according to the option chosen at the top of the panel.

  • Start—If Analyze structures from is selected, this button is displayed, and you can use it to start the scaffold decomposition job. It opens a Start dialog box, in which you can set job options and start the job.

  • Restore—If Restore results from previous run is selected, this button is displayed, and you can use it to read in the results from a previous run and display them in the Scaffold Decomposition of scaffold panel.

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