protein-prep

Goal

To prepare protein (and optionally nucleic acid) receptor structures for molecular docking (e.g., AutoDock Vina) by:

1. retrieving coordinates from RCSB PDB (optional),
2. fixing common structural issues (missing atoms, nonstandard residues),
3. adding hydrogens at a target pH.

Note: This skill handles structure cleanup and protonation. To convert the result to PDBQT for docking, use the mcp_drugdisc_convert_to_pdbqt tool.

Instructions

1. Prepare a receptor to PDB (Cleanup + Hydrogens)

This script manages missing atoms, nonstandard residues, and protonation.