fragment-based-docking-scoring/main
Version 1

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

Steps

ID Name Description
0 Number of poses Number of docking poses to generate per input compound
1 Receptor (PDB) PDB file for the receptor protein
2 All fragments (SDF) Fragments in SDF format
3 Collection size for docking Parameter for parallelization of docking
4 SuCOS threshold Value between 0 and 1. All poses with a SuCOS score lower than this value will be filtered out.
5 Fragment for SuCOS scoring (SDF/MOL) SDF or MOL file with the single fragment for SuCOS scoring
6 Candidate compounds (SMILES) List of compounds for docking in SMILES format
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
outfile outfile n/a
outfile outfile n/a
out1 out1 n/a
output output n/a
activesite activesite n/a
outfile outfile n/a
list_output_sdf list_output_sdf n/a
output output n/a
output output n/a
output output n/a
output output n/a

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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Additional credit

Simon Bray, Tim Dudgeon

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Created: 21st Sep 2022 at 08:44

Last used: 28th Sep 2022 at 17:17

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