The Atomic Coordinate Entry Format, commonly known as the PDB format, is a standard used for the representation of three-dimensional structures of molecules, particularly proteins and nucleic acids. Developed by the Protein Data Bank (PDB), this format includes detailed information about atomic coordinates, connectivity, and annotations related to molecular structures. Each entry in the PDB format is structured into sections such as header, title, primary structure, heterogen, secondary structure, connectivity, and coordinate section. The format is highly detailed, providing comprehensive metadata to support the visualization and analysis of molecular structures by the scientific community.

For more information, please refer to the official PDB format documentation.

See also: .cif

Applications that read .pdb:

  • bunch - Rigid body modelling of multidomain proteins.
  • cifop - Moves, shifts, rotates and aligns atomic and dummy atom models.
  • cifsup - Superposition of atomic and dummy atom models.
  • crysol - Calculates X-ray scattering patterns from atomic structures
  • dammif - Rapid ab-initio bead modelling
  • dammin - Ab-initio bead modelling
  • elllip - Arranges quasi-atomistic models of liposomes with elliptical shapes.
  • ffmaker - Assembles form-factor files for eom and oligomer.
  • launcher - ATSAS launcher
  • nmator - Flexible refinement in torsion-angle space.
  • oligomer - Determine volume fractions of a multi-component mixture.
  • pdb2seq - Convert atomic models to residue sequence
  • pre_bunch - Rigid body modelling of multidomain proteins.
  • sasres - Resolution assessment of models obtained from experimental data.
  • sreflex - Flexible refinement in cartesian space.

Applications that write .pdb:

  • bodies - Fit geometric shapes to SAS data; predict SAS data of geometric shapes
  • bunch - Rigid body modelling of multidomain proteins.
  • cifop - Moves, shifts, rotates and aligns atomic and dummy atom models.
  • cifsup - Superposition of atomic and dummy atom models.
  • coral - Rigid body modelling of multidomain proteins.
  • dammif - Rapid ab-initio bead modelling
  • dammin - Ab-initio bead modelling
  • elllip - Arranges quasi-atomistic models of liposomes with elliptical shapes.
  • em2dam - Converts EM-maps to dummy atom models.
  • launcher - ATSAS launcher
  • nmator - Flexible refinement in torsion-angle space.
  • pre_bunch - Rigid body modelling of multidomain proteins.
  • sreflex - Flexible refinement in cartesian space.