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

computational-chemistry-covid19-docking/workflow

Author(s)

Version
3
Last updated
Aug 31, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
computational-chemistry

Features
Tutorial
Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00032
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
output
output
output
output
outfile
outfile
outfile
outfile
list_output_sdf
activesite
output
output
output
output
output
ℹ️ Input Dataset
Candidates
ℹ️ Input Dataset
Mpro-x0195_0_apo-desolv.pdb
ℹ️ Input Dataset
hits.sdf
Enumerate changes
Compound conversion
Create Frankenstein ligand
Compound conversion
rDock cavity definition
Split file
rDock docking
Collapse Collection
XChem TransFS pose scoring
Max SuCOS score

Inputs

Input Label
Input dataset Candidates
Input dataset Mpro-x0195_0_apo-desolv.pdb
Input dataset hits.sdf

Outputs

From Output Label
Input dataset Candidates
Input dataset Mpro-x0195_0_apo-desolv.pdb
Input dataset hits.sdf
toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1 Create Frankenstein ligand

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/0.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbcavity/rdock_rbcavity/0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbdock/rdock_rbdock/0.1.4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.4.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score/0.2.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 View in ToolShed
xchem_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.

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
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. 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”
  4. Click the Import workflow button

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

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
4 cf8b1cb05 2020-08-31 01:11:11 Update some workflow names for consistency
3 60a212187 2020-06-02 07:52:35 update with covid19 tut with frankenstein ligand tool
2 2bffcbdc7 2020-03-27 10:13:37 lint
1 62d30105b 2020-03-27 09:09:18 linting covid19 cheminformatics tutorial

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