Protein Data Bank

Introduction

The Protein Data Bank (PDB) is a comprehensive repository that collects, organizes, and disseminates data on three-dimensional structures of large biological molecules, such as proteins and nucleic acids. These macromolecular structures are fundamental to the understanding of life's processes and the development of new drugs and therapies.

History

The PDB was established in 1971 as a collaborative effort between the Cambridge Crystallographic Data Centre (CCDC) and the Brookhaven National Laboratory (BNL). The idea for a public repository of protein structures was first proposed by Walter Hamilton at the 1969 Cold Spring Harbor Symposium on Protein Crystallography. The initial release included seven structures, and the database has grown exponentially since then, with over 150,000 structures as of 2020.

Data Collection and Curation

Data in the PDB is collected primarily from x-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM). Once a structure is determined, researchers can submit the data to the PDB, where it undergoes a rigorous validation process before being released to the public. The PDB also curates the data, ensuring that it is accurate, reliable, and easily accessible.

Data Format

The primary data format used in the PDB is the PDB file format, which is a text file format that provides detailed information about the structure, including atomic coordinates, secondary structure information, and connectivity information. However, the PDB has been transitioning to the more modern and flexible mmCIF format, which allows for the representation of more complex structures and data types.

Access and Use

The PDB is freely accessible to researchers and the public worldwide. Users can search the database using various criteria, such as protein name, author, or structure type. The data can be viewed in various ways, including as a three-dimensional structure or as a sequence alignment. The PDB also provides tools for comparing structures and analyzing structural relationships.

Impact and Significance

The PDB has had a profound impact on the fields of biology and medicine. It has facilitated countless discoveries in structural biology, drug design, and bioinformatics. By providing open access to structural data, the PDB has democratized science and fostered a culture of data sharing and collaboration.