PDBe, programmatically


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The Protein Data Bank in Europe (PDBe) is a member of the Worldwide Protein Databank (wwPDB), the organisation tasked with the collection, organisation and dissemination of data about biological macromolecular structures. PDBe aims to ‘bring structure to biology’ and provides a comprehensive range of tools and services to make the extensive archive of structural and functional information in the PDB more accessible to the wider biological community. You can learn more about PDBe in our webinar PDBe: Searching for biological macromolecular structures.

This webinar took place on 4th July 2017 and introduced the PDBe REST API service and show you how to access and analyse macromolecular structural data programmatically.

This webinar includes sections that focus on:

  • Introduction to the data at PDBe (1:25)
  • PDBe's RESTful API (3:33)
  • Finding additional annotation programmatically (6:30)
  • Advanced searching programmatically (11:29)
  • A simple example script (16:19)

You can download the slides, the simple script and an extra example script by using these links.

PDBe’s REST API is a programmatic way to obtain information from the PDB and EMDB. You can access details about sample, experiment, models, compounds, cross-references, publications, quality, assemblies and more.

Have a look at the following links for help and documentation:

You can also join the PDBe API user mailing list [pdbe-api-users [at] ebi.ac.uk] or get in touch with the PDBe helpdesk [pdbehelp [at] ebi.ac.uk].