Protein Data Bank (PDB)

The Protein Data Bank (PDB) as a Fundamental Resource

Overview of the PDB

The RCSB Protein Data Bank (PDB) is a worldwide database of three-dimensional structures of biological macromolecules that have been experimentally determined. PDB has more than 200,000 structures, such as proteins, nucleic acids, and complexes. The RCSB Protein Data Bank (PDB) operates and ensures the free and worldwide availability of the PDB to scientists. The PDB archive has structures that were mostly found using three experimental methods: X-ray crystallography, Nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM). When choosing structures for drug design applications, users need to think about the pros and cons of each technique in terms of resolution, size limits, and sample preparation needs.

The RCSB PDB website (https://www.rcsb.org) is widely used to access structural data. It has an easy-to-use interface for searching, visualising, and analysing this data. The website lets you search in several ways:

Text Search: Lets you search by keyword, author, protein name, or PDB ID

Sequence Search: Looks for structures that are similar to proteins or DNA sequences

Ligand Search: Finds structures that have specific small molecules or drugs in them.

Advanced Search: lets you combine several parameters to make particular queries.

The PDB-101 section (https://pdb101.rcsb.org) has educational materials for beginners, such as the "Guide to Understanding PDB Data," which explains basic ideas in structural biology. The site also has curated resources for certain topics, like viral proteins and drug targets, that can be useful starting points for drug discovery projects.