Fragment-based virtual screening with docking and pose scoring

Dock a compound library against a target protein with rDock and validate the poses generated against a reference fragment using SuCOS to compare the feature overlap. Poses are filtered by a user-specified SuCOS threshold.

A list of fragments should be specified which will be used to define the cavity for docking, using the 'Frankenstein ligand' technique. For more details, please see https://www.informaticsmatters.com/blog/2018/11/23/cavities-and-frankenstein-molecules.html

Compounds are split into collections and then recombined to allow the workflow to be run in a highly parallelized fashion. To specify the level of parallelization, use the 'Collection size' parameter.

Changelog

[0.1.5] 2023-11-20

• Fix author in dockstore

[0.1.4] 2023-02-14

Fixed

• Fix the changeset revisions for 2 tool shed repositories
• Sync version of openbabel_compund_convert step to newest version

[0.1.3] 2022-05-25

Changed

• Changed creator ORCID to absolute URI

[0.1.2] 2021-12-13

Added

• Added GitHub Actions workflow. No functional changes.

[0.1.1] 2021-12-06

Fixed

• .workflowhub.yml: use repo-name/dockstore-workflow-name scheme for workflows.
• Moved test data inside repo.

[0.1]

• Initial version of fragment-based docking and scoring workflow.

The following tools are required to run this workflow.

This will eventually be a pretty page with links to each tool in the (new) toolshed, etc.

• toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/2013.1-0+galaxy0
• toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
• toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/2020.03.4+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbcavity/rxdock_rbcavity/2013.1.1_148c5bd1+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0
• toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbdock/rxdock_rbdock/2013.1.1_148c5bd1+galaxy0
• toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2
• toolshed.g2.bx.psu.edu/repos/bgruening/sucos_docking_scoring/sucos_docking_scoring/2020.03.4+galaxy1
• toolshed.g2.bx.psu.edu/repos/bgruening/rdock_sort_filter/rdock_sort_filter/2013.1-0+galaxy0