https://github.com/ccdc-opensource/science-paper-rf-machine-learned-scoring-2022
https://github.com/ccdc-opensource/science-paper-rf-machine-learned-scoring-2022
Last synced: 5 months ago
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- Host: GitHub
- URL: https://github.com/ccdc-opensource/science-paper-rf-machine-learned-scoring-2022
- Owner: ccdc-opensource
- License: mit
- Created: 2022-03-22T11:26:29.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2025-12-16T22:55:44.000Z (6 months ago)
- Last Synced: 2025-12-20T13:22:06.652Z (6 months ago)
- Language: Python
- Size: 182 KB
- Stars: 11
- Watchers: 0
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# science-paper-rf-machine-learned-scoring-2022
---
## Docking and scoring workflows
---
### Template based docking using GOLD
To setup a docking run, generate the following files and folders:
- [docking_home]/tmp_aligned_3d_sdf_sanitized/ligand_templates_for_mcs_manual.sdf \
contains the manually curated ligand
templates in 3D. Manual curation of the templates is highly recommended to ensure proper tautomers, avoid low quality
structures
- [docking_home]/tmp_aligned_for_MOE_sanitized/*.pdb \
contains aligned protein structures from MOE projects
```bash
mkdir docking
cd docking
bsub < dock.sh
#after docking has finished
join_docked_rf_counts.py -t [target]
```
---
### Template based docking in Python
`docking.py --input_ligands ligands.sdf -t default -fr=Met713 Met712`
---
### Template based docking from MOE
One can either dock into one of the prepared projects or into an MDB of binding sites.
The binding sites MDB should have the same structure as a Roche Projects DB.
If one of the defined projects is selected, the return results will include the RF Score.
---
### Generating project specific parameters
- Series definitions are stored in rf_scoring/series_definitions/[target].json
```bash
# Change to your docking directory
cd /path/to/docking_dir
# fit RF-PLP
ccdc_roche_scoring/stat_potential.py -t pde-10
```
---
## Applications for MOE
- Start a webserver:
```bash
# LOAD ENV
moeweb -load /rf_scoring/soap_scoring_client.svl -load /template_docking/soap_template_docking_client.svl
```
- Adapt the SVL scripts to point to the webserver: \
`const SERVER_URL = 'server address';`
---
## Scoring in MOE
---
## Score an MDB of ligand poses for the active protein
---