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:

Component library menu

23 Aug 2016

Introducing the PDB Component Library

Effective data visualisation is the key to conveying the meaning of the data. At PDBe we have a variety of widgets on our pages to display protein structure data. For example, you might have seen the recently added LiteMol 3D structure viewer, or the sequence and topology diagrams which interact with it. We’ve also just added a widget indicating how PDB_Redo changes the model quality.

Screenshot of density for entry 1CBS

17 Aug 2016

Exciting visualisation update

PDBe is excited to announce some major new updates to our pages at We now have a new, streamlined 3D viewer (LiteMol) that enables visualisation of electron density in the browser with interactive changing of contour levels. For instance, check out retinoic acid in entry 1cbs.