Ligand Preparation

Goal

To prepare small-molecule ligands for molecular docking and downstream analysis by:

1. optionally enumerating relevant ligand ionization states and tautomers,
2. generating 3D conformers with RDKit ETKDG (via MCP),
3. minimizing with MMFF94/UFF (via MCP),
4. exporting a docking-ready PDBQT (AutoDock-Vina) and an optimized SDF (via MCP).

This skill combines script-based state enumeration with MCP-based 3D generation to ensure reproducibility.

Instructions

1. Enumerate States (Optional Batch Processing)

Use the script to process SMILES/SDF files and enumerate protonation/tautomer states. This outputs 2D SDFs.