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Protein Design Molecular Dynamics

Overview

PDBFixer is a software tool used to prepare and repair protein structure files for molecular simulations. It addresses common issues with Protein Data Bank (PDB) files, such as missing atoms, missing residues, and improper formatting. PDBFixer can identify these problems and automatically correct them, making the protein structures suitable for computational analyses like molecular dynamics simulations. The tool is particularly useful for ensuring that PDB files are accurate and complete before they are used in various computational chemistry and bioinformatics applications.

Neurosnap Overview

The PDBFixer online webserver allows anybody with a Neurosnap account to run and access PDBFixer, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong terms of service and privacy policy.

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Features

  • Hydrogen Addition: Automatically adds missing hydrogen atoms to protein structures, essential for molecular simulations.
  • Heavy Atom Completion: Identifies and fills in missing heavy atoms, including those in flexible regions that are often unresolved in crystallographic data.
  • Terminal Atom Fixes: Ensures terminal atoms at the ends of chains are present.
  • Nonstandard Residue Handling: Removes nonstandard residues added for crystallographic purposes that are not part of the natural molecule.
  • Selective Simulation Components: Allows users to exclude unwanted components such as salts, ligands, or multiple protein copies, focusing the simulation on the desired molecule.
  • Multiple Location Resolution: Handles cases where multiple locations are listed for some atoms, ensuring a single, accurate representation.
  • Automated Corrections: Fully automated process for fixing common issues in PDB files, saving time and reducing manual errors.
  • Explicit Solvent Addition: Adds a water box around the structure for simulations in explicit solvent environments.
  • Lipid Membrane Addition: Facilitates the addition of lipid membranes for simulations involving membrane proteins.
  • Ease of Use: User-friendly interface and straightforward commands make it accessible for users with varying levels of expertise.
  • Enhanced Simulation Accuracy: By ensuring the completeness and correctness of protein structures, PDBFixer enhances the accuracy and reliability of molecular dynamics simulations.
  • Comprehensive Problem Solving: Addresses a wide range of common issues found in PDB files, providing a one-stop solution for preparing structures for simulation.

Configuration & Options

Allowed Types: pdb, mmcif, or cif
The input protein structure (pdb or mmCIF formats) to perform repairs on using PDBFixer.

Core Settings

Find and add missing residues. The SEQRES record is referenced for the addition of missing residues.

Check this option to find and add missing heavy atoms. PDBFixer defines heavy atoms as all non-hydrogen atoms.

Check this if you want to replace non-standard residues with their standard versions.

Heterogens / hetatoms refer to molecules that are not standard amino acids or nucleotides (e.g., ligands, cofactors, ions, post-translational modifications, water molecules). PDBFixer can be configured to keep these molecules, remove all heterogens with the exception of water, or remove all heterogens including water.

Adds missing implicitly present hydrogen atoms to the structure based off of the below specified pH.

The specified pH for which to select protonation states.

Solvent Settings (Optional)

Adds a solvent / water box around your input structure. This is an optional feature for those who want to also construct a solvent box around their structure.

Type of positive ion to include in the solvent.

Type of positive ion to include in the solvent.

Desired ionic strength of the solvent. For example, if Ionic Strength=0.1, Positive Ion=K+, and Negative Ion=Cl-, then the solvent box will correspond to 0.1 molar potassium chloride. For pure water set this to 0.

The box size specifies the dimensions of the solvent box as a cube in nanometers (solvent box dimensions = box_size x box_size x box_size).

Membrane Settings (Optional)

Adds a membrane to your input structure. This is an optional feature for those who want to also construct a solvent box around their structure.

The type of lipid to use for the membrane.

The position along the Z axis at which the center of the membrane will be located in nanometers.

The minimum acceptable distance between the protein and the edges of the periodic box in nanometers.

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