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Shape screening 1

Phase Shape Screening

Use a co-crystallized ligand conformation as a query to screen a set of ligands based on the shape. Screen against several queries. Commands to run the workflow in batch.

Phase Shape Screening: Use a co-crystallized ligand conformation as a query to screen a set of ligands based on the shape. Screen against several queries. Commands to run the workflow in batch.[Requires: Phase shape] Batch execution:"$SCHRODINGER/knime" -knimeTempDir /tmp -schrodingerTempDir /tmp \-batch -nosave -stdout INFO -nosplash "-workflowFile=/home/myDir/P Shape 1.zip" \-option=8236,DataURL/0,/tmp/knime_workflow_example_data/ligands/PhaseShapeQuery.mae,String \-option=8237,DataURL/0,file:/tmp/knime_workflow_example_data/ligands/ligprepped-fragments.mae,String \-option=8231,output_file_name,/tmp/PhaseShape.mae,StringOr even simpler (after closing the workflow in the workspace):"$SCHRODINGER/run" KNIME_batch.py "<myworkspace>/2014-3/Pharmacophore/Shape screening/P Shape 1" -run -stdout INFO -istruct /tmp/knime_workflow_example_data/ligands/PhaseShapeQuery.mae -istruct1 /tmp/knime_workflow_example_data/ligands/ligprepped-fragments.mae -ostruct /tmp/PhaseShape.maeThe commands like the above can be generated automatically with: "$SCHRODINGER/run" KNIME_batch.py <myworkspace>/Pharmacophore/Shape\ screening/P\ Shape\ 1 -printcmd"$SCHRODINGER/run" KNIME_batch.py <myworkspace>/Pharmacophore/Shape\ screening/P\ Shape\ 1 -printusagedetecting tags in the node descriptions (in grey).Add the query structure in the top rowInspect the alignment of the query and the compounds similar in shape%file%Shape query%file%LigPrepped structures to screen%file%Elementatom type0.5 similarity filter EmptycellsSort by scoreRenderingShapesimilarity Concatenate Run Maestro Molecule Writer(from MAE) Molecule Reader(to MAE) Molecule Reader(to MAE) Shape Screening Row Filter Sorter Run Maestro Command Extract Properties Phase Shape Screening: Use a co-crystallized ligand conformation as a query to screen a set of ligands based on the shape. Screen against several queries. Commands to run the workflow in batch.[Requires: Phase shape] Batch execution:"$SCHRODINGER/knime" -knimeTempDir /tmp -schrodingerTempDir /tmp \-batch -nosave -stdout INFO -nosplash "-workflowFile=/home/myDir/P Shape 1.zip" \-option=8236,DataURL/0,/tmp/knime_workflow_example_data/ligands/PhaseShapeQuery.mae,String \-option=8237,DataURL/0,file:/tmp/knime_workflow_example_data/ligands/ligprepped-fragments.mae,String \-option=8231,output_file_name,/tmp/PhaseShape.mae,StringOr even simpler (after closing the workflow in the workspace):"$SCHRODINGER/run" KNIME_batch.py "<myworkspace>/2014-3/Pharmacophore/Shape screening/P Shape 1" -run -stdout INFO -istruct /tmp/knime_workflow_example_data/ligands/PhaseShapeQuery.mae -istruct1 /tmp/knime_workflow_example_data/ligands/ligprepped-fragments.mae -ostruct /tmp/PhaseShape.maeThe commands like the above can be generated automatically with: "$SCHRODINGER/run" KNIME_batch.py <myworkspace>/Pharmacophore/Shape\ screening/P\ Shape\ 1 -printcmd"$SCHRODINGER/run" KNIME_batch.py <myworkspace>/Pharmacophore/Shape\ screening/P\ Shape\ 1 -printusagedetecting tags in the node descriptions (in grey).Add the query structure in the top rowInspect the alignment of the query and the compounds similar in shape%file%Shape query%file%LigPrepped structures to screen%file%Elementatom type0.5 similarity filter EmptycellsSort by scoreRenderingShapesimilarityConcatenate Run Maestro Molecule Writer(from MAE) Molecule Reader(to MAE) Molecule Reader(to MAE) Shape Screening Row Filter Sorter Run Maestro Command Extract Properties

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On NodePit since: 2020-08-12
Last update: 2024-12-23
Created with KNIME version: v4.1.0
Tags: PharmacophorePhase shapeSchrodinger

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