PDB fixer

What is PDB Fixer?

PDB fixer is an application for preparing Protein Data Bank files for molecular simulations by automatically identifying and correcting structural issues. Built on the OpenMM molecular simulation toolkit, it addresses common crystallographic artifacts that prevent direct simulation use.

Experimental structures from X-ray crystallography frequently contain gaps and missing information. X-ray cannot resolve hydrogen atoms due to their low electron density. Flexible loops may lack electron density entirely, leaving gaps in the structure. Terminal residues often remain unmodeled. These omissions prevent direct simulation use, which requires complete atomic coordinates and explicit hydrogen placement.

PDB fixer resolves eight primary structural problems:

• Missing hydrogen atoms: adds all hydrogens absent from X-ray structures
• Missing heavy atoms: completes atoms in flexible regions with poor electron density
• Missing terminal atoms: adds atoms at chain ends
• Missing residues: builds complete loops in disordered regions
• Nonstandard residues: converts experimental modifications to standard equivalents
• Unwanted components: removes salts, buffers, duplicate chains, and other artifacts
• Alternate locations: selects single conformations when multiple positions exist
• Solvent/membrane environments: constructs water boxes or membrane bilayers for explicit solvent simulations

Reference:

• OpenMM. (2025). PDBFixer (Version 1.11) [Software]. GitHub. https://github.com/openmm/pdbfixer
• ProteinIQ. (2025). PDB Fixer [Web application]. https://proteiniq.com/utilities/pdb-fixer

Cost

Computational cost scales with atom count—small structures (2-5k atoms) process in seconds, while large complexes (15k+ atoms) may take 30-60 seconds. Adding solvent or membrane environments significantly increases processing time due to box construction and solvation calculations.

Thus, PDB Fixer uses dynamic pricing: (base + settings) × size multiplier

• Base: 2 credits per structure
• Settings: +3 solvent, +5 membrane, +2 missing residues
• Size multipliers: 1.0× (0-2k atoms), 1.25× (2-5k), 2× (5-10k), 5× (10-15k), 10× (15k+)

Examples:

• 3.5k atoms, default: 2 × 1.25 = 3 credits
• 18k atoms, default: 2 × 10 = 20 credits
• 18k atoms + solvent + membrane: (2+3+5) × 10 = 100 credits