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Docking 1-3

Docking and Scoring

Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing with Prime MM-GBSA. Build a MLR model for trying to predict the Glide score. Generate the ligand Interaction Diagrams for some poses.

[Requires: LigPrep, Glide, Prime]

Docking and Scoring: Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing with Prime MM-GBSA. Build a MLR model for trying to predict the Glide score. Generate the ligand InteractionDiagrams for some poses.[Requires: LigPrep, Glide, Prime]DescriptorsTraining and test setNo structureRemove extraneous columns %file%Plot pointlabel10 first posesRigid receptor100 ligands to dock%file%Ligands onlyInspect the Ligand Interaction diagramsPlot imagesInspect the posesP38 MAPK (1bl7)%file%1 form in 3DSD outputBuild model to predict Glide scoreswith #rotor, MW, SAS, donorHB, accptHBApply model to test setHTVSQikProp Row Splitter Column Filter Column Filter CSV Writer RowID Scatter Plot(local) Row Filter Prime MM-GBSA Smiles Reader Row Filter Image to Report Table Viewer Ligand InteractionDiagram Run Maestro Glide Grid Reader LigPrep Linear RegressionLearner RegressionPredictor Glide LigandDocking Docking and Scoring: Prepare ligands with LigPrep and dock then with Glide. Inspect the poses, perform RRHO entropy calculation and post-processing with Prime MM-GBSA. Build a MLR model for trying to predict the Glide score. Generate the ligand InteractionDiagrams for some poses.[Requires: LigPrep, Glide, Prime]DescriptorsTraining and test setNo structureRemove extraneous columns %file%Plot pointlabel10 first posesRigid receptor100 ligands to dock%file%Ligands onlyInspect the Ligand Interaction diagramsPlot imagesInspect the posesP38 MAPK (1bl7)%file%1 form in 3DSD outputBuild model to predict Glide scoreswith #rotor, MW, SAS, donorHB, accptHBApply model to test setHTVSQikProp Row Splitter Column Filter Column Filter CSV Writer RowID Scatter Plot(local) Row Filter Prime MM-GBSA Smiles Reader Row Filter Image to Report Table Viewer Ligand InteractionDiagram Run Maestro Glide Grid Reader LigPrep Linear RegressionLearner RegressionPredictor Glide LigandDocking

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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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On NodePit since: 2020-08-12
Last update: 2024-04-18
Created with KNIME version: v4.1.1
Tags: DockingLigPrepGlidePrime

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