fragment-based-docking-scoring/main
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 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

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

Added/updated 10 files


Open master cf3973d
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Simon Bray, Tim Dudgeon

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Created: 21st Sep 2022 at 08:44

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