HT4 L2: Introduction to PDB

HT4: Databases 

L2 (Lecture): Introduction to PDB

This talk will give participants an introduction to 3D macromolecular structure data in the Protein Data Bank (PDB).

The Protein Data Bank (PDB) archive is managed by the Worldwide PDB (wwPDB) consortium (wwpdb.org), who together collaborate on the development and support of the PDB archive. All experimentally determined structural biology data that is published is deposited at wwPDB. wwPDB member sites from around the world work together and coordinate data processing and weekly release of the world’s structural biology data into one single PDB repository. This repository can be accessed from any of the wwPDB member websites. 

Protein Data Bank in Europe (PDBe) is one of the founding members of the wwPDB and provides unique tools and enrichment of data to support understanding of structural biology data in the PDB archive.

This introductory talk will explore the type of data in the PDB archive, trends and changes, metrics to understand this data, the underpinning file formats, as well as some of the tools to explore the data and analyse structures.

Part of this session will be hands-on utilisation of Mol*.

Visualisation of molecular structure data is important when making assessment of structures. The focus will be on the Mol* (molstar.org) visualisation software, which allows users to view models and experimental maps within the browsers.

Learning outcomes

• How to navigate Mol* and rapidly generate presentation-ready images.
• How to retrieve and assess the quality of structural data from the PDB and EMDB archives to find the best structure for your needs.
  • Relevant metadata & validation metrics to consider.
  • Pre-populated assessment of structural features in a structure,
    for example:
    • Protein-protein interactions
    • Protein-ligand interactions