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.