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01_​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.

01_R-Group-DecompositionThis is an exercise workflow to perform R-Group Decomposition.To complete the workflow follow the instructions in the annotation boxes below.Required extensions: RDKit KNIME Integration 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 first 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 "Mol_svg" 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 second output of the Render to Images metanode. Use the Table View node andconfigure 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;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 variable MCS for the smars_value in the Flow VariablesTab 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)Connect the output port of the RDKit MCS node with the input port of the Table Row to Variable node pivot tableinput.tablecoreMCS corefirst rowmoleculesr-groups Table View Table Reader RDKit From Molecule Tile View Row Sampling Table Rowto Variable Embed images forthe R-groups Render to images Pivoting RDKit R-GroupDecomposition Pick R-groups forvisualization 01_R-Group-DecompositionThis is an exercise workflow to perform R-Group Decomposition.To complete the workflow follow the instructions in the annotation boxes below.Required extensions: RDKit KNIME Integration 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 first 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 "Mol_svg" 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 second output of the Render to Images metanode. Use the Table View node andconfigure 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;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 variable MCS for the smars_value in the Flow VariablesTab 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)Connect the output port of the RDKit MCS node with the input port of the Table Row to Variable node pivot tableinput.tablecoreMCS corefirst rowmoleculesr-groups Table View Table Reader RDKit From Molecule Tile View Row Sampling Table Rowto Variable Embed images forthe R-groups Render to images Pivoting RDKit R-GroupDecomposition Pick R-groups forvisualization

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To use this workflow in KNIME, download it from the below URL and open it in KNIME:

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Created by: daria_knime
Created at: 2020-04-16
On NodePit since: 2020-04-21
Last update: 2024-04-18
Created with KNIME version: v4.1.2

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