Annual Scientific Report 2015

(such as the on-going EMDataBank Map Challenge), and
training those new to 3DEM.
EMPIAR took off in 2015, with 37 released entries
as of December 2015, taking up over 25 TB of disk
space (the largest single entry is over 6 terabytes).
We developed and put into operation a deposition
and annotation system for EMPIAR data, as well as a
volume-slice viewer that will become available for all
EMDB entries in early 2016. Our team began work on
adding support for imaging modalities other than 3DEM
and electron tomography; we released the first such
datasets in January 2016. In the context of the MRC/
BBSRC-funded MOL2CELL project, of which
EMPIAR is one component, we also organised a
very productive expert workshop to discuss 3D
segmentations and transformations.
Outreach
The new PDBe website offers several new useful
and powerful tools, which are only useful if people
know about them and use them. The launch was
accompanied by communication, outreach and
training activities, including: roadshows (in Newcastle,
UK; Hamburg, Germany; Umeå, Sweden; Helsinki,
Finland), presentations and posters at conferences
(e.g. presentation and exhibition at the ECM
conference in Croatia), webinars, engaging social
media announcements, leaflets, newsletters, lectures
in courses at universities, co-organisation of the
EMBL-EBI Structural Bioinformatics training course,
invited lectures in Europe and beyond, and new tutorials
and modules for Train Online. We also hosted dozens
of visitors and participants in workshops and meetings.
In 2015, our Facebook following grew to over 4000,
and our Twitter followers now number over 3300, an
increase by around 50% for both in just one year. PDBe
team members published six papers in peer-reviewed
journals, and served as ambassadors for EMBL-EBI
and PDBe.
Gerard Kleywegt
Protein Data Bank in Europe (PDBe)
PhD University of Utrecht, 1991. Postdoctoral
researcher, then independent investigator,
University of Uppsala, 1992-2009. Co-ordinator,
then Programme Director of the Swedish
Structural Biology Network, 1996-2009.
Research Fellow of the Royal Swedish Academy
of Sciences, 2002-2006. Professor of Structural
Molecular Biology, University of Uppsala, 2009.
At EMBL-EBI since 2009.
Future plans
Feedback about the new PDBe website from the user
community has been overwhelmingly positive. In
2016 we will build on this success and provide more
data (especially pertaining to ligands and validation),
tools (e.g., an easy-to-use viewer for X-ray electrondensity
maps for PDB entries, a volume-slice viewer
for EMDB entries) and new search features. Following
the public release of the joint wwPDB D&A system in
January 2016, we will begin to implement the entire
system at all wwPDB sites; the old and new systems will
operate in parallel until all structure depositions can
be handled via the new system. We will also work with
our wwPDB partners to provide validation reports for
all structures in the PDB archive (planned for public
release in Q2 2016). In 2016 we will strive to reflect
the rapid developments in the field of 3D bioimaging
in our support of the archiving, analysis (including
visualisation and validation) and dissemination of data
related to 3D cellular structure at levels, from molecules,
complexes, organelles and cells to small samples.
Selected publications
Gutmanas A, et al. (2015) NMR Exchange Format: a
unified and open standard for representation of NMR
restraint data. Nat. Struct. Mol. Biol. 22:433-434
Lewis TE, et al. (2015) Genome3D: exploiting structure
to help users understand their sequences. Nucleic Acids
Res. 43:D382-D3866
Sali A, et al. (2015) Outcome of the First wwPDB hybrid/
integrative methods task force workshop. Structure
23:1156-1167
Wood C, et al. (2015) Collaborative computational
project for electron cryo-microscopy. Acta Crystallogr.
D71:123-126
EMPIAR, the archive for raw EM images data,
had 37 entries as of December 2015.
2015 EMBL-EBI Annual Scientific Report 108