Substitutability Score Analysis Panel

This panel presents information on what other known drug-like molecules have the same substitutions as a result from a core hopping run. If there are many other molecules with the same substitution points, it is considered more likely that the selected result molecule can be synthesized.

To open this panel, click Substitutability Analysis in the Visualize Results tab of the Ligand-Based Core Hopping panel.

  • Using
  • Features
  • Additional Resources

Using the Substitutability Score Analysis Panel

When a molecule is displayed in the Workspace, the database is searched for the core SMILES pattern. If it is found in a structure, the attachment points of the core in this structure are examined to see if there are any non-hydrogen groups (R groups, or substitutions) at the attachment points. If there are, it is considered to be a substitution pattern, even if not all the attachment points are substituted.

To use this panel, you must have available in the project a set of results from a core-hopping run whose input structures came from an .sqlite database.

  1. Open the .sqlite database used to find the cores that you are visualizing in the Visualize Results tab.

  2. Display one of the results in the Workspace.

    The structure is analyzed and displayed in the Result structure section of the panel. If the substitution score is not zero, substitution patterns are displayed in the substitution pattern table

  3. Use the left or right arrow keys on the Project Table panel or the Workspace to step through the structures in your results set until you display one that has a substitution pattern.

  4. Click on one of the substitution patterns.

    An example of a known structure that has this substitution pattern is displayed in the Sample parent structure area, with a substitutability score and the number of times it was found.

Substitutability Score Analysis Panel Features

 

Select core database used with run text box and Browse button

Select the .sqlite database that you used to find the selected core-hopping result. The database contains the substitution information that is required to run the analysis.

Result structure display

This area displays the 2D structure of the core-hopping result that is displayed in the Workspace. If you change the result in the Workspace, an analysis is performed on the new structure. The structure you display in the Workspace must be one of the results of the search using the specified database.

Sample parent structure display

This area displays the 2D structure of a sample compound that contains the selected pattern in the substitution pattern table.

Substitution pattern table

This table lists the substitution patterns found in the database, represented with R at the attachment points. Clicking a pattern displays an example of the pattern in the Sample parent structure display area.

Related Topics