pdb
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.
- coral - Rigid body modelling of multidomain proteins.
- crysol - Calculates X-ray scattering patterns from atomic structures
- cryson - Calculates neutron scattering patterns from atomic structures.
- dammif - Rapid ab-initio bead modelling
- dammin - Ab-initio bead modelling
- dammix - Ab-initio bead modelling of intermediate states
- elllip - Arranges quasi-atomistic models of liposomes with elliptical shapes.
- ffmaker - Assembles form-factor files for eom and oligomer.
- flexbin - Quaternary structure modeling of a dimeric complex.
- gasbori/gasborp - Ab-initio dummy residue modelling
- gasbormx - Ab-initio dummy residue modelling for oligomeric equilibria
- globsymm - Modelling of oligomeric structures.
- launcher - ATSAS Application launcher
- monsa - Ab-initio bead modelling of multiple phases.
- nmator - Flexible refinement in torsion-angle space.
- nmawrapper - Calculate normal modes of biological macromolecules.
- oligomer - Determine volume fractions of a multi-component mixture.
- parcoor - Partitions a high-resolution structural model into pseudo-domains.
- pdb2seq - Convert atomic models to residue sequence
- pre_bunch - Rigid body modelling of multidomain proteins.
- ranch - Random chain generation
- sasref - Modelling of multisubunit complexes.
- sasrefcv - Rigid body modelling of multisubunit complexes against contrast-variation SAS data.
- sasrefmx - Rigid body modelling of multisubunit complexes from polydisperse SAXS data.
- 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
- dammix - Ab-initio bead modelling of intermediate states
- elllip - Arranges quasi-atomistic models of liposomes with elliptical shapes.
- em2dam - Converts EM-maps to dummy atom models.
- flexbin - Quaternary structure modeling of a dimeric complex.
- gasbori/gasborp - Ab-initio dummy residue modelling
- gasbormx - Ab-initio dummy residue modelling for oligomeric equilibria
- globsymm - Modelling of oligomeric structures.
- launcher - ATSAS Application launcher
- monsa - Ab-initio bead modelling of multiple phases.
- nmator - Flexible refinement in torsion-angle space.
- parcoor - Partitions a high-resolution structural model into pseudo-domains.
- pre_bunch - Rigid body modelling of multidomain proteins.
- ranch - Random chain generation
- sasref - Modelling of multisubunit complexes.
- sasrefcv - Rigid body modelling of multisubunit complexes against contrast-variation SAS data.
- sasrefmx - Rigid body modelling of multisubunit complexes from polydisperse SAXS data.
- sreflex - Flexible refinement in cartesian space.