PDBDatei

A PDB file, also known as a Protein Data Bank file, is a standard file format used in bioinformatics and structural biology to store information about the three-dimensional structure of proteins, nucleic acids, and complex assemblies. The PDB format was developed by the Protein Data Bank (PDB), an international repository of biological macromolecular structures, and has become the de facto standard for sharing and archiving structural data.

PDB files contain a variety of information, including atomic coordinates, secondary structure assignments, and details about the experimental methods used to determine the structure. The file format is plain text and consists of a series of records, each starting with a four-letter code that identifies the type of information contained in the record. Common record types include ATOM, HETATM, and CONECT, which provide details about atoms, heteroatoms, and connectivity, respectively.

PDB files are widely used in molecular modeling, drug discovery, and structural bioinformatics. They can be generated from experimental data, such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy, or from computational methods, such as homology modeling or molecular dynamics simulations. PDB files can be visualized and analyzed using a variety of software tools, including PyMOL, Chimera, and VMD.

The PDB format has evolved over time to accommodate new types of data and experimental techniques. The latest version of the PDB format, PDBx/mmCIF, is based on the Crystallographic Information File (CIF) format and provides a more flexible and extensible framework for storing and sharing structural data. Despite these advances, the classic PDB format remains widely used and continues to be an essential tool for structural biology and bioinformatics.