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Binding Poses and Energies Calculation

This workflow calculates binding poses and energies between peptides and all-atom models of adsorbent surfaces. For detailed information about the methods used and to see a use case of the workflow, please refer to the provided link below.

Before running the workflow, configure all nodes in the "Input" box. You can enter multiple docking grids of adsorbent surfaces and SMILES representations of peptides. Please note that the workflow is compatible only with Schrödinger Release 2023-2.

After the workflow completes, the binding energies are written to an Excel file and saved in the specified directory. The binding poses are imported into a Maestro project; ensure you provide the path in the "Run Maestro" node.

Input Output Load GridsStart Loop:For Every Grid-FileLoop to get4 binding posesper target moleculeStart Loopto CalculateBinding EnergiesStart loopfor every target moleculeImport poses inSchrödingerRead SMILES file Glide Grid Reader Prime MM-GBSA Loop End Counting Loop Start Input - Variables Counting Loop Start MarcoModelMinimization Generic Loop Start Loop End Delete OverlappingPoses Save Resultsas XLSX Variable ConditionLoop End Glide Docking LigPrep GFN2-xTB-Single-Point-Engery- Loop End PrepareDocking Input Truncate Model Group Loop Start Run Maestro Smiles Reader Input Output Load GridsStart Loop:For Every Grid-FileLoop to get4 binding posesper target moleculeStart Loopto CalculateBinding EnergiesStart loopfor every target moleculeImport poses inSchrödingerRead SMILES file Glide Grid Reader Prime MM-GBSA Loop End Counting Loop Start Input - Variables Counting Loop Start MarcoModelMinimization Generic Loop Start Loop End Delete OverlappingPoses Save Resultsas XLSX Variable ConditionLoop End Glide Docking LigPrep GFN2-xTB-Single-Point-Engery- Loop End PrepareDocking Input Truncate Model Group Loop Start Run Maestro Smiles Reader

Nodes

Extensions

Links

Download

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

Download Workflow
Created by: gx7288
Created at: 2024-01-06
On NodePit since: 2024-10-20
Last update: 2024-11-21
Created with KNIME version: v4.7.1

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