The Agent Skills Directory

[COMMAND_EXECUTION]: The skill uses the Python subprocess module to execute the prodigy command-line utility. The arguments are passed as a list, which is a secure practice that prevents shell injection vulnerabilities.
[EXTERNAL_DOWNLOADS]: The skill identifies prodigy-prot as a dependency to be installed via pip. This is the standard distribution method for this well-known bioinformatics tool.
[DATA_INGESTION_SURFACE]: The skill accepts Protein Data Bank (PDB) files as input for processing. These are structured scientific data files typically processed by the PRODIGY tool, and there is no evidence of unsafe interpolation of these files into LLM prompts.

binding-affinity-prediction-prodigy