PDBFixer

Updated: Nov 19, 2024


Latest versions

1.2.2 for SAMSON 2024 R1

1.2.2 for SAMSON 2024 R1

1.2.2 for SAMSON 2024 R1

535
14

Free extension

Free
No credit card required

PDBFixer

Updated: Nov 19, 2024


Latest versions

1.2.2 for SAMSON 2024 R1

1.2.2 for SAMSON 2024 R1

1.2.2 for SAMSON 2024 R1

535
14
Fix problems in PDB files in preparation for simulating them: remove alt.locations, add missing resides and atoms, add solvent and membrane, etc.

This extension integrates the PDBFixer Python package and exposes its functionality.

PDBFixer fixes issues in Protein Data Bank (PDB) files (supported formats: PDB, mmCIF/PDBx) in preparation for simulating them. It can fix the following problems:

  • Add missing heavy atoms.
  • Add missing hydrogen atoms.
  • Build missing loops.
  • Convert non-standard residues to their standard equivalents.
  • Select a single position for atoms with multiple alternate positions listed.
  • Delete unwanted heterogens.
  • Build a water box for explicit solvent simulations.
  • Build a membrane around a protein.

References

[1] PDBFixer Python package. https://github.com/openmm/pdbfixer

[2] Eastman P. et al. (2017). OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLOS Computational Biology, 13(7), e1005659. https://doi.org/10.1371/journal.pcbi.1005659

PDBFixer is an extension for SAMSON,
the integrative platform for molecular design.

To use PDBFixer:

1. Create your free account and choose a molecular design plan
2. Download and install SAMSON on your computer
3. Come back to this page to add the extension to your account


When you restart SAMSON, the extension will be automatically installed
and will be usable directly from within SAMSON.