Protein Data Bank

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Protein structure examples

Rate of Protein Structure Determination-2019b

Protein Data Bank (PDB) is a comprehensive, publicly accessible database that archives three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, primarily obtained through X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy, are critical for understanding the molecular architecture of biological macromolecules and their roles in various biological processes. This information is invaluable for research in biochemistry, molecular biology, pharmacology, and medicine.

History

The Protein Data Bank was established in 1971 as a collaborative effort by researchers in the USA and Europe. Its creation was motivated by the growing need for a centralized repository to store the structural data of proteins for easy access and sharing within the scientific community. Over the years, the PDB has grown from a small collection of structures to a vast, globally accessible database that is essential for the study of biological systems at the molecular level.

Data Format and Access

The primary data format used by the PDB is the PDB file format, which provides detailed information about the atomic positions, chemical bonds, and molecular geometry of each structure. In addition to the original PDB format, the database also supports the mmCIF format, which offers a more comprehensive and flexible structure for representing molecular data.

Access to PDB data is provided through various means, including the PDB website, which offers search and visualization tools for exploring the structures. Additionally, several software tools and libraries are available for analyzing and working with PDB data, facilitating a wide range of scientific research activities.

Importance in Scientific Research

The Protein Data Bank is a crucial resource for scientists in many fields. It enables researchers to elucidate the three-dimensional structures of biological macromolecules, understand their function and dynamics, and explore how proteins interact with each other and with other molecules, such as DNA, RNA, and small ligands. This understanding is fundamental for the development of new drugs, as it allows for the identification of molecular targets and the design of molecules that can modulate the activity of specific proteins.

Challenges and Future Directions

Despite its success, the PDB faces several challenges, including the need to accommodate the rapidly growing volume of structural data and the increasing complexity of the structures being deposited. There is also a continuous effort to improve the quality and consistency of the data in the database. Future directions for the PDB include enhancing data standardization, improving user interfaces, and integrating with other biological data resources to provide a more comprehensive view of biological systems at the molecular level.

See Also

• X-ray crystallography
• NMR spectroscopy
• Cryo-electron microscopy
• Bioinformatics
• Structural biology