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Tests 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 |
|
| Candidate compounds (SMILES) | Candidate compounds (SMILES) | List of compounds for docking in SMILES format |
|
| Collection size for docking | Collection size for docking | Parameter for parallelization of docking |
|
| MOL) | Fragment for SuCOS scoring (SDF/MOL) | SDF or MOL file with the single fragment for SuCOS scoring |
|
| Number of poses | Number of poses | Number of docking poses to generate per input compound |
|
| Receptor (PDB) | Receptor (PDB) | PDB file for the receptor protein |
|
| SuCOS threshold | SuCOS threshold | Value between 0 and 1. All poses with a SuCOS score lower than this value will be filtered out. |
|
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 |
|
| Scored and filtered poses | Scored and filtered poses | n/a |
|
Version History
Version 1 (earliest) Created 21st Sep 2022 at 08:44 by Simone Leo
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Created: 21st Sep 2022 at 08:44
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