PDBrestore

PDBrestore repairs raw PDB files for molecular dynamics simulations by adding hydrogen atoms, completing side chains, filling sequence gaps, and generating solvated simulation boxes.

Key Features:

• Hydrogen addition: Adds hydrogen atoms to protein structures.
• Side chain completion: Completes missing atoms in side chains.
• Sequence gap filling: Fills gaps in the protein sequence.
• Ligand parameter generation: Derives the itp parameter file for a ligand according to the GAFF2 force field for GROMACS applications.
• Simulation box generation: Generates a reasonably pre-equilibrated solvated simulation box.

Scientific Applications:

• Drug design: Prepares initial protein-ligand coordinates for drug design projects such as free energy perturbation or thermodynamic integration calculations of ligand binding affinities.
• Molecular dynamics simulations: Streamlines preparatory work for setting up protein structures for molecular dynamics simulations.

Methodology:

Processes protein PDB chains extracted from either a local PDB file or a PDB file downloaded from the Protein Data Bank.