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

## TL;DR

PDBrestore is a free web tool that fixes issues in raw PDB files to prepare them for molecular dynamics simulations and drug design.

## Contribution

PDBrestore introduces an automated web interface for repairing PDB files with minimal user input.

## Key findings

- PDBrestore adds hydrogen atoms and completes missing atoms in side chains.
- It generates pre-equilibrated simulation boxes for use in drug design projects.
- The tool is available as both a web interface and a command-line application.

## Abstract

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.

PDBrestore is a freely accessible web interface to repair raw PDB files fetched from the Protein Data Bank for molecular dynamics applications. The interface, with minimal end‐user intervention, repairs common PDB defects such as missing atoms, incomplete side chains, missing residues, non‐standard residue names or non‐standard atom labels, manages the presence of cofactors, ligands, or post‐translational modifications such as disulfide bridges, and provides a pre‐equilibrated simulation box including explicit solvent.