The PREPARE Program
Protein Rotamers Evaluation and Protonation based on Accurate Residue Energy
PREPARE is a tool for automated protein preparation and optimization from pdb files directly to mol2 protein and ligand files.
- Reads PDB files
- Identifies residues, ligand, co-factors, metals
- Adds hydrogens
- Assigns charges, atom types
- Evaluates rotamers and various protonation states simultaneously
- Optimizes water molecule orientation
- Outputs standard mol2 files
More details about the PREPARE program can be found in the references.