CABSdock client

Automate the submission of jobs to the CABS-dock server for flexible protein-peptide docking.

Usage

Submit jobs:

./cabsdock.py SFGDGFADF sample/pdb_codes.txt

• SFGDGFADF is the ligand sequence.

• pdb_codes.txt is a file containing the pdb receptors, one per line.

If the PDB file is not found in pdb_codes.txt's directory, it will be downloaded from the PDB.

The output is a list of URLs for the submitted jobs. You can redirect the output to a file in order to use it later with cabsdownload.

Download results:

./cabsdownload.py sample/submitted_jobs.txt

• submitted_jobs.txt is a list of job URLs that were submitted to the CABSdock server. This list is normally generated by running cabsdock.

If a job is successfully completed, its results are download. In case the job is still running, the program retries from time to time. The results are downloaded to the input file's directory.