HT3 L4: Programmatic access of macromolecular structure data

HT3: Databases

L4 (Lecture): Programmatic access of macromolecular structure data


David Armstrong
Protein Data Bank in Europe (PDBe)
European Bioinformatics Institute (EMBL-EBI)
E-mail: [email protected]

If you are looking to access large volumes of PDB data for your own analyses, the best way for quick and automated access is to do it programmatically, instead of going through the website. PDBe has developed a set of REST APIs that provide easy access to high-quality information regarding biomacromolecular structures archived in PDB.


These APIs provide a simple, reliable, lightweight mechanism to:

  • Query macromolecular structure data
  • Select entries or molecules of interest and access targeted information about them
  • Access information on the molecules, experimental details, assemblies, motifs, function, taxonomy, structure quality, etc.


There is more information on the various PDBe APIs at


PDBe also has a dedicated webinar series on programmatic access:


This talk will give an introduction to how to programmatically access data in the PDB. It will also highlight how this data is used on PDBe and PDBe-KB pages as a case study for the use of the PDBe APIs. It will also introduce the PDB component library which provides access to web components developed by PDBe to visualize structural data.