PDBrestore: A Free Web Interface for Processing and Fixing Protein Chains From Raw PDB Files

We present PDBrestore, a free web interface for repairing protein PDB chains extracted from either a local PDB file or a PDB file downloaded from the Protein Data Bank. PDBrestore performs several key tasks: It adds hydrogen atoms, completes missing atoms in side chains, fills gaps in the sequence, derives the itp parameter file for a ligand according to the GAFF2 force field for GROMACS applications, and generates a reasonably pre-equilibrated solvated simulation box. The interface is designed to streamline the cumbersome preparatory work required to set up an initial protein-ligand coordinates PDB file for use in drug design projects, such as free energy perturbation or thermodynamic integration calculations of ligand binding affinities. Additionally, PDBrestore is available as a command-line application within the open-source ORAC distribution, which can be freely downloaded from the website: www1.chim.unifi.it/orac.