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Training

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]

Inspect the posesInspect the structures in 2Dand the postprocessing resultsRigid receptorLigands only%file%100 ligands to dock%file%P38 MAPK (1bl7)%file%1 form in 3DSD outputHTVS 10 structures FEP+ readerLambda 16,20,28 Command,subjobsCheckthe calculationis running LabeldG to pKi FEP mapper:clear all predictionsFEP+ panelFEP calculations dG to pKi Ligand Waters1ETT Atoms by chain Ligand representation See workflow examples Run Maestro Table Viewer Prime MM-GBSA Row Filter Molecule Writer(from MAE) Smiles Reader Glide Grid Reader LigPrep Glide LigandDocking Smiles Reader RDKit From Molecule RDKit Add Hs Export toLiveDesign LiveDesignConnection Molecule-to-MAE Import fromLiveDesign Extract Properties Extract Properties FEP+ reader Run FEP+ Table Viewer ChemistryExternal Tool Row Filter Row Splitter Concatenate Column Appender Joiner RowID ConstantValue Column Table Creator Python Script 1:1 Table Viewer ChemistryExternal Tool ChemistryExternal Tool FEP+ Reader(deprecated) Python Script 1:1 Table Viewer Split by Structure Delete Atoms Get PDB Extract Atom/bondProperties GroupBy Molecule-to-MAE Protein PreparationWorkflow Run Maestro Run Maestro Command CSV Writer Excel Writer Column Filter Upload asLiveDesign Model Inspect the posesInspect the structures in 2Dand the postprocessing resultsRigid receptorLigands only%file%100 ligands to dock%file%P38 MAPK (1bl7)%file%1 form in 3DSD outputHTVS 10 structures FEP+ readerLambda 16,20,28 Command,subjobsCheckthe calculationis running LabeldG to pKi FEP mapper:clear all predictionsFEP+ panelFEP calculations dG to pKi Ligand Waters1ETT Atoms by chain Ligand representation See workflow examplesRun Maestro Table Viewer Prime MM-GBSA Row Filter Molecule Writer(from MAE) Smiles Reader Glide Grid Reader LigPrep Glide LigandDocking Smiles Reader RDKit From Molecule RDKit Add Hs Export toLiveDesign LiveDesignConnection Molecule-to-MAE Import fromLiveDesign Extract Properties Extract Properties FEP+ reader Run FEP+ Table Viewer ChemistryExternal Tool Row Filter Row Splitter Concatenate Column Appender Joiner RowID ConstantValue Column Table Creator Python Script 1:1 Table Viewer ChemistryExternal Tool ChemistryExternal Tool FEP+ Reader(deprecated) Python Script 1:1 Table Viewer Split by Structure Delete Atoms Get PDB Extract Atom/bondProperties GroupBy Molecule-to-MAE Protein PreparationWorkflow Run Maestro Run Maestro Command CSV Writer Excel Writer Column Filter Upload asLiveDesign Model

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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: 2024-02-22
Last update: 2024-12-21
Created with KNIME version: v4.7.1
Tags: DockingLigPrepGlidePrime

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