Protein preparing tool provides a function to extract ligands from binding site and protonate the protein structure , and shows ligand coordinate and radius information with PDB file downloaded from PDB website. This tool is divided into 2 steps.

Step1. Submit a PDB file downloaded from PDB website.

Step2. It will give the information of ligand's coordinate and radius, protonated protein file and a parameter which can adjust binding site radius by contect protein atoms.