Use PDBFixer Online

PDBFixer: Automated Repair of Protein Data Bank Files for Molecular Simulation

PDBFixer is an easy-to-use application for fixing problems in Protein Data Bank files so they are ready for molecular dynamics simulation. It accepts PDB or PDBx/mmCIF structures and automatically adds missing atoms and residues, replaces nonstandard residues, removes unwanted molecules, and can build a water box or membrane around the system. PDBFixer is part of the OpenMM project, with copyright held by Peter Eastman and Stanford University (2013-2025), and is distributed as an open repository on GitHub.

Experimental structures are rarely simulation-ready. X-ray crystallography usually does not resolve hydrogens, flexible loops can be missing entirely, and crystallographers often add nonstandard residues, salts, ligands or extra copies of the protein that are not part of the natural molecule. Some atoms are also listed with multiple alternate positions. A simulation engine cannot start from such a file without careful cleanup, and doing that by hand is slow and error-prone.

PDBFixer addresses these problems in a fully automated way, so a raw structure from the PDB can be turned into a clean, consistent input for explicit-solvent or membrane simulations.

What PDBFixer Repairs in Protein Structure Files

The manual lists the following problems that PDBFixer can fix:

• Missing heavy atoms: from a few sidechain atoms up to entire loops in flexible regions, including missing atoms at chain termini.

• Missing hydrogens: added for a chosen pH, selecting the most common protonation state at that pH.

• Nonstandard residues: replaced with standard equivalents, either suggested or user-chosen.

• Unwanted content: remove chains, and keep all heterogens, keep only water, or delete all heterogens.

• Alternate locations: a single position is selected for atoms listed with several.

• Solvent and membranes: add a water box with counterions, optional extra ions set by ionic strength, or a POPC or POPE membrane for membrane proteins.

How PDBFixer Works: Workflow and Options

In the desktop interface the workflow runs through seven pages in order.

1. Load File: choose a local file or enter a PDB ID to download from RCSB.

2. Select Chains: remove chains and choose how heterogens are handled.

3. Add Residues: missing residues inferred from SEQRES records are listed, and you select which to add.

4. Convert Residues: replace nonstandard residues.

5. Add Heavy Atoms: list and add missing heavy atoms.

6. Add Hydrogens, Water and Membrane: set pH, solvent box, ions or membrane.

7. Save File: write the processed structure.

Command-line options

Python API

For full control, the Python API exposes each step, such as finding missing residues and atoms, replacing nonstandard residues, removing heterogens, adding hydrogens, and adding solvent or a membrane. Methods must be called in the documented order, and the lists of missing residues and atoms can be edited before they are applied.

What is Tamarind Bio?

Tamarind Bio is a no-code bioinformatics platform built to give life scientists and researchers access to powerful computational tools. Many cutting-edge machine learning models are hard to deploy and use. Tamarind provides an intuitive, web-based environment that removes the complexity of high-performance computing, software dependencies and command-line interfaces.

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• A user-friendly graphical interface for setting up and launching experiments

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• An automated system for managing and scaling computational resources

Tamarind treats information and data security as a top priority, as detailed in its Trust Center and Terms of Service.

Accelerating Discovery with PDBFixer on Tamarind Bio

• Simulation-ready structures: prepare crystal structures for molecular dynamics by filling gaps and adding hydrogens at a chosen pH.

• Cleaner inputs for modeling: strip salts, ligands, extra chains and alternate locations so downstream tools see a consistent structure.

• Solvated and membrane systems: add a water box with neutralizing ions, or embed a membrane protein in a POPC or POPE bilayer.

• Nonstandard residue handling: convert modified residues to standard equivalents.

How to Use PDBFixer on Tamarind Bio

1. Open the tool: log in to tamarind.bio and open PDBFixer.

2. Provide a structure: upload a PDB or PDBx/mmCIF file, or supply a PDB ID if exposed.

3. Choose chains and heterogens: decide which chains to keep and whether to keep all heterogens, only water, or none.

4. Set repair options: if exposed, enable adding missing residues and replacing nonstandard residues.

5. Set hydrogens and solvent: pick the pH (default 7.0) and, if exposed, a water box, ion types and ionic strength, or a membrane.

6. Run the job: submit and wait for the repaired structure.

7. Download and inspect: download the processed PDB file and check that the changes match what you intended.

8. Use downstream: feed the cleaned structure into simulation, docking or structure-prediction analysis.

Things to Keep in Mind

• Missing residues are not added unless explicitly requested on the command line.

• Missing residues are inferred from SEQRES records, so files without them cannot be completed this way.

• Added residues and loops are built automatically, so they should be checked before relying on them.

• When adding a membrane, do not also add a separate water box.

• The manual does not state a citation or license type; check the repository for current terms.

Source: PDBFixer Manual, OpenMM project (Peter Eastman, Stanford University), https://htmlpreview.github.io/?https://github.com/openmm/pdbfixer/blob/master/Manual.html. Code: https://github.com/openmm/pdbfixer.