snakemake-cartesian-ddg

Snakemake pipeline for Rosetta cartesian-ddg application for the prediction of protein stability change (ddG) upon mutation.

Quickstart

1. Configure paths to your Rosetta binary (ROSETTABIN) and DB (ROSETTADB) in config.yaml.

2. Place your PDB file in pdb directory and configure target_pdbs in config.yaml.

3. Prepare mutfiles corresponding to mutations for which you want to measure ddG values.

4. Configure mutfiles in config.yaml. Note that * means that all mutfiles in the directory will be used.

5. Run the pipeline.

$ snakemake -pr -j[NUM_CORES]

Pipeline overview