PREPARE, a tool for protein preparation and optimization.

 Protein Rotamers Evaluation and Protonation based on Accurate Residue Energy

-  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
-  Superposes and makes multiple pdb files similar for flexible protein docking with FITTED
-  Outputs standard mol2 files