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Validate parameters 1-3

Validate Docking Parameters

Prepare and concatenate a set of co-crystallized, known active, and inactive compounds. Dock them with Glide SP and XP to compare the results using an enrichment plot and a ROC curve. Do the same comparisons after post-processing the results with Prime MM-GBSA.

[Requires: Glide, LigPrep, Prime]

Validate Docking Parameters: Prepare and concatenate a set of co-crystallized, known active, and inactive compounds. Dock them with Glide SP and XP to compare the results using an enrichment plot and a ROC curve. Do the samecomparisons after post-processing the results with Prime MM-GBSA.[Requires: Glide, LigPrep, Prime]Enrichment curve in Openoffice or ExcelAlter the rendering and inspect visually the posesCompare docking settings Area under the curveLigands in tube Proteinligands%file%Known active compounds%file%Inactive compounds%file%Cocrystallized active compounds%file%1ac4%file%Enrichment plotSPXPPrime MM-GBSA ROC Curve (local) Run SpreadsheetViewer ROC Curve (local) Run Maestro Table Viewer Table Viewer Run Maestro Command Post processing Concatenate Best by ligand Prime MM-GBSA ROC Curve (local) ROC Curve (local) Best by ligand report Row Splitter CSV Writer Post processing Ligand preparation Smiles Reader Smiles Reader Molecule Reader(to MAE) Glide Grid Reader EnrichmentPlotter (local) Glide LigandDocking Glide LigandDocking Validate Docking Parameters: Prepare and concatenate a set of co-crystallized, known active, and inactive compounds. Dock them with Glide SP and XP to compare the results using an enrichment plot and a ROC curve. Do the samecomparisons after post-processing the results with Prime MM-GBSA.[Requires: Glide, LigPrep, Prime]Enrichment curve in Openoffice or ExcelAlter the rendering and inspect visually the posesCompare docking settings Area under the curveLigands in tube Proteinligands%file%Known active compounds%file%Inactive compounds%file%Cocrystallized active compounds%file%1ac4%file%Enrichment plotSPXPPrime MM-GBSA ROC Curve (local) Run SpreadsheetViewer ROC Curve (local) Run Maestro Table Viewer Table Viewer Run Maestro Command Post processing Concatenate Best by ligand Prime MM-GBSA ROC Curve (local) ROC Curve (local) Best by ligand report Row Splitter CSV Writer Post processing Ligand preparation Smiles Reader Smiles Reader Molecule Reader(to MAE) Glide Grid Reader EnrichmentPlotter (local) Glide LigandDocking 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: 2020-02-17
Last update: 2020-02-26
Created with KNIME version: v4.1.0
Tags: DockingGlideLigPrepPrime

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