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Macrocycle strain Energy

Low energy conformations

It runs a MacroModel or ConfGen conformational search on structures prepared with LigPrep. Optionally align them on a reference to inspect the conformational spaces in the context of the binding site.

[32162] 21.2.1
See details on https://kni.me/w/eAckV-NVB9b9o_rG

Compound structure input protocolNew LiveReport column(s):- Relative energy 2 macrocycles Cyclic peptide#atoms Fastutilities/phase_align_core -noflex ? MobileEach structure Energy Each structureTitleTitle RemoveduplicateligandsCorporate ID Upload asLiveDesign Model Column Filter Math Formula LiveDesignConnection Get PDB Protein PreparationWorkflow Split by Structure Row Splitter Extract Properties Prime MacrocycleSampling Get Help Table Viewer Ligand Alignment Run Maestro RMSD Chunk Loop Start Loop End GroupBy Sorter Column Appender Extract Properties Loop End Chunk Loop Start Group MAE Extract Properties Ungroup MAE Column Renamer LiveDesign Input GroupBy Column Renamer LigPrep MAE-to-SD Compound structure input protocolNew LiveReport column(s):- Relative energy 2 macrocycles Cyclic peptide#atoms Fastutilities/phase_align_core -noflex ? MobileEach structure Energy Each structureTitleTitle RemoveduplicateligandsCorporate ID Upload asLiveDesign Model Column Filter Math Formula LiveDesignConnection Get PDB Protein PreparationWorkflow Split by Structure Row Splitter Extract Properties Prime MacrocycleSampling Get Help Table Viewer Ligand Alignment Run Maestro RMSD Chunk Loop Start Loop End GroupBy Sorter Column Appender Extract Properties Loop End Chunk Loop Start Group MAE Extract Properties Ungroup MAE Column Renamer LiveDesign Input GroupBy Column Renamer LigPrep MAE-to-SD

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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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Created by: jcmozzic
Created at: 2020-01-31
On NodePit since: 2024-07-16
Last update: 2024-11-18
Created with KNIME version: v5.2.1
Tags: LiveDesignLigPrepMacroModelConfGenSchrodinger

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