Workflow Type: Galaxy

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.

Inputs

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

Steps

ID Name Description
7 Compound conversion toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0
8 Create Frankenstein ligand toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand/2013.1-0+galaxy0
9 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
10 Enumerate changes toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges/2020.03.4+galaxy0
11 rDock cavity definition toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbcavity/rxdock_rbcavity/2013.1.1_148c5bd1+galaxy0
12 Compound conversion toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0
13 Split file toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0
14 rDock docking toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbdock/rxdock_rbdock/2013.1.1_148c5bd1+galaxy0
15 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2
16 Score docked poses using SuCOS toolshed.g2.bx.psu.edu/repos/bgruening/sucos_docking_scoring/sucos_docking_scoring/2020.03.4+galaxy1
17 rDock docking toolshed.g2.bx.psu.edu/repos/bgruening/rdock_sort_filter/rdock_sort_filter/2013.1-0+galaxy0

Outputs

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

Version History

v0.1.4 (latest) Created 17th Feb 2023 at 03:01 by WorkflowHub Bot

Updated to v0.1.4


Frozen v0.1.4 062e4e0

v0.1.2 Created 21st Dec 2021 at 03:01 by WorkflowHub Bot

Updated to v0.1.2


Open master e42d116

v0.1.1 Created 7th Dec 2021 at 03:01 by WorkflowHub Bot

Updated to v0.1.1


Frozen master db0c104

v0.1 (earliest) Created 4th Dec 2021 at 03:00 by WorkflowHub Bot

Added/updated 9 files


Frozen master 8a02b10
help Creators and Submitter
Creators
  • Simon Bray
  • Tim Dudgeon
Additional credit

Simon Bray, Tim Dudgeon

Submitter
License
Activity

Views: 2310

Created: 4th Dec 2021 at 03:00

Last updated: 17th Feb 2023 at 03:01

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