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

Area of Science:

• Computational chemistry
• Structural biology
• Drug discovery

Background:

• Preparing protein-ligand complexes for molecular simulations is a complex and time-consuming process.
• Accurate initial structures are crucial for reliable computational predictions of ligand binding affinities.

Purpose of the Study:

• To present PDBrestore, a user-friendly web interface and command-line tool for repairing and preparing protein PDB files.
• To streamline the generation of protein-ligand complex structures for drug design simulations.

Main Methods:

• PDBrestore adds hydrogen atoms, completes missing side-chain atoms, and fills sequence gaps.
• It generates ligand parameter files using the GAFF2 force field for GROMACS.
• The tool creates pre-equilibrated, solvated simulation boxes.

Main Results:

• PDBrestore automates key steps in preparing protein-ligand PDB files.
• It facilitates the setup of structures for advanced computational methods like free energy perturbation and thermodynamic integration.
• The tool is available as a free web interface and a command-line application within the ORAC distribution.

Conclusions:

• PDBrestore significantly simplifies and accelerates the preparation of protein-ligand complexes for computational drug design.
• The tool enhances the accessibility of molecular simulation studies by automating tedious preparatory tasks.