PDBrestore is a simple web interface for repairing protein PDB chains extracted from a local PDB file or a PDB file downloaded from the Protein Data Bank . PDBrestore adds the hydrogen atoms, the missing atoms of side chains, fills the gaps in the sequence, produces the itp parameters of a ligand according to GAFF2 force field , and produces a reasonably pre-equilibrated solvated simulation BOX. The interface is aimed at alleviating the cumbersome preparatory work for setting up a starting protein+ligand coordinates PDB file to be used in drug design projects (e.g. FEP or TI calculations of ligand binding affinities). The interface can process only one protein chain at a time and supports only protein-ligand systems . DNA or RNA chains are not supported. PDBrestore as a command-line application is available in the ORAC distribution.