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.

15 Aug 2016

PDBe deposition maintenance 26-30 Aug

The wwPDB deposition system at PDBe will be unavailable between 26 and 30 August due to essential site maintenance.

Depositors from Europe and Africa will be redirected to our RCSB PDB partner site from 22 August until the end of the maintenance to start new deposition sessions. Ongoing depositions at PDBe will not be accessible during the maintenance period (26-30 August).

Validation percentile plot

09 Aug 2016

wwPDB Validation Server Upgrade

The new wwPDB Validation Server at now generates preliminary validation reports for structures solved by NMR and 3D Electron Microscopy, in addition to X-ray crystallography.

wwPDB strongly encourages the use of the Validation Server at any time during the structure determination process, but particularly when preparing structures for deposition to the wwPDB. Validation Server reports provide identical information to the ones generated at deposition.

Some of the wwPDB annotation staff from Europe, Japan and the USA who will process newly deposited structural data for PDB, EMDB and BMRB

31 May 2016

AutoDep, EMDep deposition systems no longer accept new depositions

From the 31st May 2016, the legacy deposition systems, AutoDep, ADIT-NMR (BMRB|PDBj) and EMDep, will no longer accept new PDB and EMDB submissions. Depositors with in-progress sessions on the legacy systems will be able to access and complete their deposition sessions until the 25th August 2016
Stephen Curry playing with one of his poliovirus structures at PDBe

27 Apr 2016

Laughing out loud with Stephen Curry

Structural biologist and Guardian blogger Stephen Curry visited EMBL-EBI to inspire our scientists and engineers to get writing. PDBe’s Maya Holmdahl reports.
PDBe's powerful new graphics display

26 Apr 2016

Powerful graphics workstation for exploring big imaging data

PDBe’s new high-performance graphics workstation allows its biocurators to work with large-scale 3D electron microscopy datasets, exploring macromolecular structures seamlessly from every angle.
MOL2CELL - archiving structural data on scales from molecules to cells

05 Apr 2016

The big picture - 3D structure from molecules to cells

Recently, a paper describing PDBe’s new volume slicer was published in the Journal of Structural Biology. The slice viewer is a web-based tool that allows scientists to look in detail at 3D bioimaging datasets. It is the first step in the development of an integrated browser that will allow visualisation, integration and analysis of 3D structural data on scales from molecules to cells. The development of this integrated browser is part of PDBe’s MOL2CELL project. Gerard Kleywegt tells you more.
The PDBe team and their visitors from EMBL-Hamburg

23 Mar 2016

Hamburg days at PDBe

This week, the PDBe team at EMBL-EBI hosted no fewer than seven structural biology colleagues from EMBL-Hamburg.

Detail of the webpage for entry EMPIAR-10055

21 Mar 2016

EMPIAR supports "Method of the Year"

The official announcement of EMPIAR in Nature Methods prompts Gerard Kleywegt, Head of the Protein Data Bank in Europe, to reflect on the origins and future directions of this essential resource for raw biomolecular imaging data.