Version 1

Workflow Type: Galaxy
Tests: Passing

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

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.


ID Name Description Type
All fragments (SDF) All fragments (SDF) Fragments in SDF format
  • File
Candidate compounds (SMILES) Candidate compounds (SMILES) List of compounds for docking in SMILES format
  • File
Collection size for docking Collection size for docking Parameter for parallelization of docking
  • int
MOL) Fragment for SuCOS scoring (SDF/MOL) SDF or MOL file with the single fragment for SuCOS scoring
  • File
Number of poses Number of poses Number of docking poses to generate per input compound
  • int
Receptor (PDB) Receptor (PDB) PDB file for the receptor protein
  • File
SuCOS threshold SuCOS threshold Value between 0 and 1. All poses with a SuCOS score lower than this value will be filtered out.
  • float


ID Name Description
7 Compound conversion
8 Create Frankenstein ligand
9 Compose text parameter value
10 Enumerate changes
11 rDock cavity definition
12 Compound conversion
13 Split file
14 rDock docking
15 Collapse Collection
16 Score docked poses using SuCOS
17 rDock docking


ID Name Description Type
Docking poses Docking poses n/a
  • File
Scored and filtered poses Scored and filtered poses n/a
  • File

Version History

Version 1 (earliest) Created 21st Sep 2022 at 08:44 by Simone Leo

Added/updated 10 files

Open master cf3973d
help Creators and Submitter
Not specified
Additional credit

Simon Bray, Tim Dudgeon


Views: 137

Created: 21st Sep 2022 at 08:44

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