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R-group Decomposition

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Kelly Bachovchin

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

1.png

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

2.png

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

3.png

 

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

4.png

 

Plot Settings

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

 

6.png

 

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

7.png

 

 

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.

 

RgroupAsAxes_May2023.gif