ABFE Workflow is a pipeline variant of our prior work.
Project description
ABFE_workflow
WARNING: The repo is currently under development - No Guarantees at the moment. But will be soon at a first version. This goes with a manuscript, that is currently submitted. :)
A snakemake based workflow for ABFE calculations using GMX. The workflow can be scaled on Slurm Queuing systems. The here provided Cyclophilin D Test systems and experimental values originate from:
- Alibay, I.; Magarkar, A.; Seeliger, D.; Biggin, P. C. Evaluating the use of absolute binding free energy in the fragment optimisation process. Communications Chemistry 2022, 5, 105.
- Grädler, U.; Schwarz, D.; Blaesse, M.; Leuthner, B.; Johnson, T. L.; Bernard, F.; Jiang, X.; Marx, A.; Gilardone, M.; Lemoine, H.; Roche, D.; Jorand-Lebrun, C. Discovery of novel Cyclophilin D inhibitors starting from three dimensional fragments with millimolar potencies. Bioorganic Medicinal Chemistry Letters 2019, 29, 126717.
Here a visualization of the triggered process:
New Features:
We are currently improving the user experience. The input was simplified to simply only the need of providing a pdb file for the receptor and .sdf files for the ligand.
>cli-abfe -h
usage: cli-abfe [-h] -p PROTEIN_PDB_PATH -l LIGAND_SDF_DIR -o OUTPUT_DIR_PATH [-c COFACTOR_SDF_PATH] [-nc NUMBER_OF_CPUS_PER_JOB] [-nj NUMBER_OF_PARALLEL_JOBS] [-nr NUMBER_OF_REPLICATES] [-submit]
[-gpu] [-hybrid]
optional arguments:
-h, --help show this help message and exit
-p PROTEIN_PDB_PATH, --protein_pdb_path PROTEIN_PDB_PATH
Input protein pdb file path
-l LIGAND_SDF_DIR, --ligand_sdf_dir LIGAND_SDF_DIR
Input ligand(s) sdf file path
-o OUTPUT_DIR_PATH, --output_dir_path OUTPUT_DIR_PATH
Output approach folder
-c COFACTOR_SDF_PATH, --cofactor_sdf_path COFACTOR_SDF_PATH
Input cofactor(s) sdf file path
-nc NUMBER_OF_CPUS_PER_JOB, --number_of_cpus_per_job NUMBER_OF_CPUS_PER_JOB
Number of cpus per job
-nj NUMBER_OF_PARALLEL_JOBS, --number_of_parallel_jobs NUMBER_OF_PARALLEL_JOBS
Number of jobs in parallel
-nr NUMBER_OF_REPLICATES, --number_of_replicates NUMBER_OF_REPLICATES
Number of replicates
-nosubmit Will not automatically submit the ABFE calculations
-nogpu don't use gpus for the submissions?
-nohybrid don't do hybrid execution (complex jobs on gpu and ligand jobs on cpu (requires gpu flag))
Usage:
An example usage is provided with the examples/example_execution.sh
, that uses the ABFE_Calculator.py
script.
If you remove the submit flag, you can a start a run, that only sets up the folder structure. (checkout our example folder)
Additional script information is provided via:
conda activate abfe
cli-abfe -h
# or
cli-abfe-gmx -h
Running an ABFE Campaign from Bash:
conda activate abfe
cli-abfe -p <path>/receptor.pdb \
-l <path>/myligands \
-o <path>/Out \
-nogpu -nohybrid -nc 8
Input
The input is suggested to be structured as follows for the commandline option:
- <ligands>
- ligand1.sdf
- ligand2.sdf
- ligand3.sdf
- ...
- receptor.pdb
For the python call:
- ligand_sdfs:List[str] - paths to sdf files
- protein_pdb_path: str - path to pdb file
Alternativley you can provide gromacs input files and use the command line tool ABFE_GMX_CLI
. Please make sure your ligand is called LIG
in the gmx files. The input sturucture should look like this:
- <rooot_dir>
- <ligand-1>
- solvent
- solvent.gro
- solvent.top
- complex
- complex.gro
- complex.top
- solvent
- <ligand-2>
- solvent
- solvent.gro
- solvent.top
- complex
- complex.gro
- complex.top ...
- solvent
- <ligand-1>
Install:
The package can be installed like the following script:
cd ABFE_workflow
conda env create --file ./environment.yml
conda activate abfe
pip install .
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