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04_​R-Group_​Decomposition

02_R-Group_Decomposition

This is an exercise workflow to perform R-Group Decomposition.

To complete the workflow follow the instructions in the annotations.
I. Compute MCS.
II. Perform R-Group Decomposition.
III. Find how many molecules with each combination of the two selected R-groups are in the dataset.
IV. Create a component to visualize the results of the R-group decomposition.




04_R-Group-DecompositionThis is an exercise workflow to perform R-Group Decomposition.To complete the workflow follow the instructions in the annotation boxes below. IV. Create a component to visualize the results of the R-group decomposition.Execute all preceding nodes in the workflow first.The view should have 4 elements: 1. The pivoted table in which the row headers represent the first R-group and the column headers represent the second R-group. The Table View node "pivot table" is already configured.Execute the node and open the interactive view (Right Click > Execute and Open Views). Explore the Table.2. The images of the molecules displayed like tiles. The images are available from the output of the Render to Images metanode. Use the Tile View node and configure it: - Options Tab: fix number of tiles per row to 1; choose a title column to show compound_chembl_id; include columns "pIC50" and the column with the svg of the molecule to display; - Interactivity Tab: set initial page size to 1; enable "Show selected rows only"; - Formatters Tab: Enable global number format to 2 decimal places.3. Image of the MCS. The Tile View "MCS core" node is already configured. Execute the node and explore the view.4. The table with the images of the R-groups of selected molecules. The images are available from the output of the Render to Images metanode. Use the Table View node and configure it: - Options Tab: select the column with compound_chembl_id and the columns with the svg images of the R-groups to display; - Interactivity Tab: enable "Show selected rows only".Create a component encapsulating these Views: - Select the Table View node with the pivot table, the Row Sampling node, the Tile View node with image of the molecule, the Tile View node with the MCS image, and the Table Viewnode with the images of the R-groups; - Right click on one of the selected nodes and chose "Create Component"; - Execute the Component and explore the view (Right Click > Execute and Open Views). Optional:Configure the layout of component - open the component (Ctrl/CMD + double click); - open the Node Usage and Layout Editor by clicking on the corresponding icon in the Toolbar; - rearrange the elements: the pivoted table at the top; the image of the molecule and the image of the MCS side by side below the pivoted table; and the table with R-groups in thebottom; - apply the changes; go back to the main workflow and execute component once again to explore the changes in the layout. III. Find how many molecules with each combination of the two selected R-groups are in thedataset.Execute all preceding nodes in the workflow first.Configure the Pivoting node using flow variables carrying the column names with the selected R-groups:- Available flow variables can be found in the output of the preceding node (Pick R-groups forvisualization component) in the Flow Variables Tab - Open configuration dialog of the Pivoting node- Groups Tab: include one column (e.g. R1); Pivots Tab: include one column (e.g. R2)- Manual Aggregation Tab: Add column with pIC50 values and aggregate their count- Tick to "enable hiliting" option in the bottom of the dialog- Flow Variables Tab: choose Rgroup1 for InclList variable in the grouByColumns; choose Rgroup2 forInclList variable in the pivotColumns;- In the Advanced Settings: Set column name to “pivot name”Execute the Pivoting node and explore the output table II. Perform R-Group DecompositionExecute all preceding nodesConfigure the RDKit R-Group Decomposition node to usethe MCS as the scaffold in the configuration dialogHint: Make sure to connect the output of the RDKit MCSnode to the RDKit R-Group Decomposition node I. Compute MCSExecute the Table Reader nodeUse the RDKit MCS node (find it in the Node Repository) to compute the MCS for the molecules in thedataset.Configure the node: - to match a fraction of the molecules (e.g. 0.8); - the ring atoms match only ring atoms; - to match valences.Execute the node (e.g. F7) and explore its output (e.g. right-click -> MCS of the input structures) I. Explore the output of the sketcher component II. Perform R-Group Decomposition Add the RDKit R-Group Decomposition node andconnect it to the output of the Table Reader. Connectthe core drawn with the Sketcher component to theoptional input. Investigate the output coreMCS corefirst rowinput.tablefor the pivoted tablepivot tablemolecules and R-groups RDKit From Molecule Tile View Row Sampling Pivoting RDKit R-GroupDecomposition Pick R-groups forvisualization Molecular Sketcher Table Reader Embed images of picked R-groupsin column headers and row headers Table View Render to images 04_R-Group-DecompositionThis is an exercise workflow to perform R-Group Decomposition.To complete the workflow follow the instructions in the annotation boxes below. IV. Create a component to visualize the results of the R-group decomposition.Execute all preceding nodes in the workflow first.The view should have 4 elements: 1. The pivoted table in which the row headers represent the first R-group and the column headers represent the second R-group. The Table View node "pivot table" is already configured.Execute the node and open the interactive view (Right Click > Execute and Open Views). Explore the Table.2. The images of the molecules displayed like tiles. The images are available from the output of the Render to Images metanode. Use the Tile View node and configure it: - Options Tab: fix number of tiles per row to 1; choose a title column to show compound_chembl_id; include columns "pIC50" and the column with the svg of the molecule to display; - Interactivity Tab: set initial page size to 1; enable "Show selected rows only"; - Formatters Tab: Enable global number format to 2 decimal places.3. Image of the MCS. The Tile View "MCS core" node is already configured. Execute the node and explore the view.4. The table with the images of the R-groups of selected molecules. The images are available from the output of the Render to Images metanode. Use the Table View node and configure it: - Options Tab: select the column with compound_chembl_id and the columns with the svg images of the R-groups to display; - Interactivity Tab: enable "Show selected rows only".Create a component encapsulating these Views: - Select the Table View node with the pivot table, the Row Sampling node, the Tile View node with image of the molecule, the Tile View node with the MCS image, and the Table Viewnode with the images of the R-groups; - Right click on one of the selected nodes and chose "Create Component"; - Execute the Component and explore the view (Right Click > Execute and Open Views). Optional:Configure the layout of component - open the component (Ctrl/CMD + double click); - open the Node Usage and Layout Editor by clicking on the corresponding icon in the Toolbar; - rearrange the elements: the pivoted table at the top; the image of the molecule and the image of the MCS side by side below the pivoted table; and the table with R-groups in thebottom; - apply the changes; go back to the main workflow and execute component once again to explore the changes in the layout. III. Find how many molecules with each combination of the two selected R-groups are in thedataset.Execute all preceding nodes in the workflow first.Configure the Pivoting node using flow variables carrying the column names with the selected R-groups:- Available flow variables can be found in the output of the preceding node (Pick R-groups forvisualization component) in the Flow Variables Tab - Open configuration dialog of the Pivoting node- Groups Tab: include one column (e.g. R1); Pivots Tab: include one column (e.g. R2)- Manual Aggregation Tab: Add column with pIC50 values and aggregate their count- Tick to "enable hiliting" option in the bottom of the dialog- Flow Variables Tab: choose Rgroup1 for InclList variable in the grouByColumns; choose Rgroup2 forInclList variable in the pivotColumns;- In the Advanced Settings: Set column name to “pivot name”Execute the Pivoting node and explore the output table II. Perform R-Group DecompositionExecute all preceding nodesConfigure the RDKit R-Group Decomposition node to usethe MCS as the scaffold in the configuration dialogHint: Make sure to connect the output of the RDKit MCSnode to the RDKit R-Group Decomposition node I. Compute MCSExecute the Table Reader nodeUse the RDKit MCS node (find it in the Node Repository) to compute the MCS for the molecules in thedataset.Configure the node: - to match a fraction of the molecules (e.g. 0.8); - the ring atoms match only ring atoms; - to match valences.Execute the node (e.g. F7) and explore its output (e.g. right-click -> MCS of the input structures) I. Explore the output of the sketcher component II. Perform R-Group Decomposition Add the RDKit R-Group Decomposition node andconnect it to the output of the Table Reader. Connectthe core drawn with the Sketcher component to theoptional input. Investigate the output coreMCS corefirst rowinput.tablefor the pivoted tablepivot tablemolecules and R-groups RDKit From Molecule Tile View Row Sampling Pivoting RDKit R-GroupDecomposition Pick R-groups forvisualization Molecular Sketcher Table Reader Embed images of picked R-groupsin column headers and row headers Table View Render to images

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Created by: daria_knime
Created at: 2020-04-16
On NodePit since: 2024-01-14
Last update: 2024-11-21
Created with KNIME version: v4.6.0
Tags: Maximum Common Substructure (MCS)SketcherR-Group-Decomposition (RGD)RDKitChemoinformaticsLife SciencesEducation

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