Looking back on 2016

Looking back on 2016
16 January 2017

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”).

In 2016 we celebrated the 20th anniversary of what was originally called the Macromolecular Structure Database at EMBL-EBI. In 2009, it was renamed Protein Data Bank in Europe (PDBe). As of 2017, the team that deals with the EMDB and EMPIAR archives will operate as a separate entity (internally, we call it the Cellular Structure and 3D Bioimaging team, led by Ardan Patwardhan). We expect this team to grow over the next few years as EMBL is focusing on digital biology (in which imaging plays a major role), and EBI aspires to become a global hub for archiving imaging data. The team that deals with the PDB archive will continue to be called Protein Data Bank in Europe (led by Sameer Velankar). Together we make up EMBL-EBI’s Molecular and Cellular Structure cluster.

25,000 PDB structures annotated (and counting)

In 2016, we annotated our 25,000th PDB structure! This comes only 5 1/2 years after annotating our 10,000th structure and the major cause of the acceleration is the fact that we now annotate all structures that come in from Europe and Africa. Furthermore, EMDB reached the milestone of 4,000 entries and, more impressively, released over 1,000 structures in 2016 alone (1,027, compared to 640 in 2015), and the PDB released its 1,000th EM/ED model. In 2016, the PDB received 11,614 structure depositions, of which 4,050 (35%) were annotated at PDBe. EMDB received 1074 depositions, of which 337 (31%) were annotated here. EMPIAR received 30 new datasets (including the largest dataset so far, of beta-galatosidase at 2.2Å resolution, with over 12 TB of image data), compared to 21 in 2015. These also included the first 3DSEM datasets, i.e. entries not available in EMDB.

In January 2016, the new unified deposition system for PDB/EMDB/BMRB structural data (OneDep) was rolled out, accommodating X-ray/neutron/electron diffraction, EM and NMR depositions. All the legacy deposition systems (for us, AutoDep and EMdep) were closed down after the summer. One of the advantages of the new system is that it produces validation reports for all new depositions. Moreover, wwPDB released validation reports for all legacy NMR and EM structures in the archive, so that basic validation information is now available for all PDB entries.

Our raw EM image data archive, EMPIAR, was officially announced. It was discussed in various editorials and blogs (e.g., here, here and here).

Reaching out

A structural biology paper that drew a lot of attention worldwide (after all, how often do you see an EM map in The Daily Mail?) was that describing the Zika virus structure. Within 10 minutes of the Science paper going on-line, PDBe had made it its featured structure.

As usual, our staff engaged in numerous outreach and training events, from courses to roadshows to conferences (~50 events in 2016), to spread the word about our work, resources, services etc. Furthermore we published a number of papers describing our work (and that of our collaborators): 11 in 2016. We produced a very popular 2017 calendar with beautiful, original artwork related to biomacromolecular structure and health and disease in developing countries. And thanks to the hard work of our social media enthusiasts, our Facebook following grew from ~4000 to ~5400 in 2016, while our Twitterati audience increased from ~3300 to ~4600! We regularly host visitors as well. Amongst the 2016 visitors was a large delegation of our EMBL Hamburg colleagues, as well as structural bloggologist Stephen Curry who gave a well-attended seminar for the campus.

Of course many more things happened, including the release of many new features on the websites (including interactive density viewing for all X-ray and EM structures that have experimental data in PDB or EMDB). You can read our archive of news items or scroll through our postings on Facebook and Twitter.

Thank you!

We thank all our depositors, users and of course funders (EMBL-EBI, Wellcome Trust, BBSRC, MRC, NIH, EU and CCP4) for their continued support! We hope you will continue to use our services in 2017, and we look forward to your feedback and suggestions, either in person at roadshows, conferences, etc., through our social media outlets, through the “Feedback” button on our web pages, or just by plain old email. And if you like the services we provide, please tell your colleagues, students, etc. about them!