David Stuart seminar at EMBL-EBI

03 Feb 2017

David Stuart visit to EMBL-EBI

On Friday 3 February 2017, Prof. David Stuart FRS FMedSci visited EMBL-EBI to discuss issues of common interest regarding the structural biology archives PDB, EMDB and EMPIAR, and how metadata collected at large experimental facilities could be captured and archived better. Prof. Stuart is an MRC Research Professor, joint Head of the Structural Biology Division at the University of Oxford, Director of Instruct (the European research infrastructure for structural biology), and Life Sciences Director at the Diamond Light Source.

SCCEM and EBI representatives who discussed mirroring EM data in China

19 Jan 2017

EM archives to be mirrored in China

This week, a delegation from the Society of Chinese Cryo Electron Microscopy (SCCEM) visited EMBL-EBI to discuss how cryo-EM data in EMDB and EMPIAR could be made available to users from within China.

Looking back on 2016

16 Jan 2017

Looking back on 2016

Gerard Kleywegt looks back at some of the past year’s highlights in the world of PDBe, EMDB and EMPIAR in his slog (“sometime blog”).

Electron density for all!

09 Jan 2017

Electron density for all!

In his first "slog" ("sometime blog") of 2017, Gerard Kleywegt explains why it is useful to look at electron-density maps, what those blue, red and green chicken-wire objects mean, and how you can view maps from the comfort of your own browser at PDBe, without any need to download software or data.

You can read the blog here:

Electron density for retinoic acid in PDB entry 1CBS

13 Dec 2016

Uppsala Electron Density Server to be retired

After  serving the scientific community with electron-density maps for two decades, the Uppsala Electron Density Server (EDS; is now reaching the end of its life cycle and will be retired some time in 2017. The good news is that much of the EDS functionality (and in particular the delivery of map and mtz files, as well as a much better 3D viewer) is now provided by PDBe.

PDBe's 2017 Calendar

30 Nov 2016

PDBe 2017 Calendar

Our 2017 calendar features artwork inspired by the proteins connected with health and disease in developing countries.
Screenshot of PDBe PyMOL plugin

10 Oct 2016

Plugin shows structure annotations in PyMOL

There’s lots of extra data in a PDB entry that isn’t shown in many viewers, making it difficult to view and analyse. PDBe’s PyMOL plugin helps out with this problem by displaying some of this extra information in PyMOL.

Structural Bioinformatics training course 2016

28 Sep 2016

Structural Bioinformatics training course 2016

Last week, the annual Structural Bioinformatics training course was held in the EMBL-EBI training facilities ( A mix of students, post-docs etc.

Awarding the PDBe poster prize at ECM30

02 Sep 2016

PDBe Poster Prize winner at ECM30

Congratulations to Almudena Ponce-Salvatierra, a PhD student from the Max Planck Institute for Biophysical Chemistry. Almudena won the Protein Data Bank in Europe (PDBe) poster prize at the 30th meeting of the European Crystallographic Association (ECM-30) in Basel, Switzerland.

20 Years of PDBe

01 Sep 2016

20 Years of PDBe

To mark the 20th birthday of EMBL-EBI's Protein Data Bank in Europe resource (although it was initially called the Macromolecular Structure Database, MSD), Rosemary Wilson has written "Form follows function", which looks at the importance of PDBe and the archives it manages, as well as its links with the Hamburg laboratory of EMBL: