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04 May 2017

SIFT-ing through sequence space in the PDB

You’ve probably noticed that many of the protein structures in the PDB archive are cross-referenced to other data resources. These cross-references, for example to UniProt, Pfam, CATH and SCOP are displayed on our website, and on those of our wwPDB partners.

Poster prize winners

12 Apr 2017

BSG David Blow Poster Prize awarded

Congratulations to Amirul Adli Bin Abdul Aziz who won the BSG David Blow Poster Prize, sponsored by PDBe, at the British Crystallographic Association Spring Meeting in Lancaster yesterday. The trophy comprises a piece of Blue John crystal mounted on an oak plinth.

Full-immersion exploration of 3D structure with Molecular Rift (photo credit: Magnus Norrby)

15 Mar 2017

Virtual Reality to interact with 3D structures

Although VR (virtual reality) has been around for decades, it is only now with cheap and powerful hardware (compuers, headsets and smartphones), and demand from the world of gaming, that VR applications are becoming more widely available. On 14 March 2017, we were visited by Jonas Boström (whose day job is in computational chemistry at AstraZeneca in Mölndal, Sweden) and a former student of his, Magnus Norrby (who now works for the Nordea bank) to discuss possible applications of VR.

Artist and scientist in front of painting of protein structure

06 Mar 2017

Bringing Artists and Scientists Together Creates Very Exciting Results

A recent collaboration between scientists from the PDBe team, local arts societies Camdfas and Grantadfas, and arts students in local schools has led to some amazing results. One is currently on display in a Cambridge gallery.

 Map showing wwPDB Regional Data Center workload distribution

09 Feb 2017

The paper describing wwPDB OneDep system is now available

The paper describing wwPDB OneDep system is now available. The wwPDB has deployed a unified system for deposition, biocuration, and validation of macromolecular structures globally across all wwPDB, EMDB, and BMRB deposition sites to meet the evolving requirements of the scientific community to archive structural data over the coming decades.

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.