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
mkdir docking
cd docking
bsub < dock.sh
#after docking has finished
join_docked_rf_counts.py -t [target]docking.py --input_ligands ligands.sdf -t default -fr=Met713 Met712
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.
- Series definitions are stored in rf_scoring/series_definitions/[target].json
# Change to your docking directory
cd /path/to/docking_dir
# fit RF-PLP
ccdc_roche_scoring/stat_potential.py -t pde-10- Start a webserver:
# 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';