Workflows

These workflows are associated with Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

Virtual screening of the SARS-CoV-2 main protease with rDock and pose scoring

Last updated Aug 31, 2020

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Tests: ❌ Results: Not yet automated

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flowchart TD
  0["ℹ️ Input Dataset\nCandidates"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nMpro-x0195_0_apo-desolv.pdb"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nhits.sdf"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Enumerate changes"];
  0 -->|output| 3;
  4["Compound conversion"];
  1 -->|output| 4;
  5["Create Frankenstein ligand"];
  2 -->|output| 5;
  6["Compound conversion"];
  3 -->|output| 6;
  7["rDock cavity definition"];
  4 -->|outfile| 7;
  5 -->|outfile| 7;
  8["Split file"];
  6 -->|outfile| 8;
  9["rDock docking"];
  4 -->|outfile| 9;
  8 -->|list_output_sdf| 9;
  7 -->|activesite| 9;
  10["Collapse Collection"];
  9 -->|output| 10;
  11["XChem TransFS pose scoring"];
  1 -->|output| 11;
  10 -->|output| 11;
  12["Max SuCOS score"];
  11 -->|output| 12;
  2 -->|output| 12;

Importing into Galaxy

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
Hands-on: Importing a workflow
  • Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
  • Click on Import at the top-right of the screen
  • Provide your workflow
    • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
    • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
  • Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure: