CDD Vault Visualization provides an R-group decomposition plot for Molecules loaded into Visualization. Whether you're sending data from your private, secure CDD Vault or importing a data file into the Visualization tool, you are able analyze core structures and their various R-group attachments.
Once your data is loaded into the CDD Vault Visualization tool and structures are analyzed, a “plot type” for R-group decomposition is available. After clicking the R plot users can choose one of two options:
- Select a core from one of the SuperSAR fragments
- Draw a “core” and R-group attachment points in the structure editor
A scatter plot is then generated with the R1 and R2 substituents plotted on the X and Y axes. Three columns for the core, R1, and R2 structures are added to the report table underneath.
Creating an R-group decomposition plot
- Select the R-group decomposition plot in the toolbar at the top of the visualization session
Select a core from the SuperSAR fragments
- SuperSAR will suggest core groups based on the structures uploaded to the visualization session
- You can use your mouse to scroll through the suggestions and choose one as the core structure
Launching the structure editor to draw a core
- If you cannot find the core you are looking for in the suggestions you can draw your own
- Click "Launch the Structure editor"
- Draw the core structure
- Use the "R1" button in the toolbar to add the R1 and R2 groups to the structure
Interacting with the plot
- Use your mouse or track pad to zoom in and out of the plot
- As you zoom in, the R-group structures will start to display on the axes
- Hovering your mouse over a point will show the corresponding structure
- Clicking on a point will pull up the molecule and all the corresponding data from the table
- "Shift"+clicking on a point will paste the structure into the plot area
Any settings applied to the plot will be viewable in a collapsible legend in the plot area. Select the parameter to map a column of data to on the right-hand side of the screen.
- Change the color of plotted points
- Change the shape of plotted points
- Change the size of plotted points
- Sort the R1 or R2 structures on the axes by a specific value
Structure columns in the report table
- Three columns are added to the data table for the Core, R1, and R2 structures
- Click on the column header to sort the structures by their structural similarity
Helpful hint: Once you've created an R-group Decomposition plot and selected your desired core, the R1 and R2 groups can be assigned to the x-axis of a Scatter plot.