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

Run Workflow in Galaxy

• Galaxy Main
• Galaxy Europe
• Galaxy Australia
• Galaxy France
• Import to another server (≥23.0+ only!)

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;

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.

Importing into Galaxy

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 galaxy-upload 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:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/covid19-docking/workflows/workflow.ga -O workflow.ga
workflow-to-tools -w workflow.ga -o tools.yaml
shed-tools install -g GALAXY -a API_KEY -t tools.yaml
workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows