An automated configuration script for anchored docking using AutoDock-GPU.
Note: This project is still under development.
This script provides a simplified setup for performing anchored docking as described in the AutoDock-GPU Anchored Docking Guide. By overlaying ligands that share a core, it functions as an alternative to core-constrained docking.
While this method may be useful for applications like relative binding free energy perturbation calculations, please note that it has not been experimentally validated.
The requirements are the same as those listed in the Anchored Docking Guide.
- RDKit
- Meeko==0.6.1
- ADFR
- AutoDock-GPU
- AutoGrid
- Download and extract
scripts.zipfrom theAnchored Docking Guide.- Since the above page has been removed, please download
write-gpf.pyfrom https://github.com/diogomart/write-autogrid-config, and downloadaddbias.pyandinsert_type_in_fld.pywith reference to ccsb-scripps/AutoDock-GPU#283. Place these files in thescriptsdirectory. Note that these download links are temporary and likely to change in the future.
- Since the above page has been removed, please download
As a test case, we provide an anchored docking tutorial for the Bace1 receptor.
Run the following command:
python anchored_docking.py \
--template_file test/crystal_ligand.sdf \
--input_file test/CAT-13f.sdf \
--receptor_file test/Bace1_protein.pdb \
--docking_dir test/output- green: receptor (Bace1)
- cyan: template ligand (CAT-4j)
- magenta: docked CAT-13f
- yellow: CAT-13f Pose used in Wang-FEP-dataset