New chemistry images at PDBe

01 Nov 2018

Bringing clarity to chemistry at PDBe

The PDB is an archive of macromolecular structures, but the small molecules bound in these structures are the focus of much interest. We have recently made some changes to the way we display images of small molecules at PDBe, which brings a lot more clarity to their chemistry.

ECM Poster Prize presentation

26 Aug 2018

ECM31 Poster Prize Awarded

Congratulations to Sasa Petrovic (left) from Max Delbrück Center for Molecular Medicine and Marie Haufroid from Université de Namur who were awarded the PDBe sponsored poster prize at the European Crystallographic Meeting in Oviedo, Spain.

They are shown receiving their prize from PDBe's David Armstrong (right).

Many thanks to Prof. Maria Joao Romao, Prof. Randy Read, Dr. Martin Bommer, Dr. Yvette Roske, Dr. Kevin Cowtan and Dr. Martin Walsh for their help in judging the poster prize.

PDBe raw experimental data component

02 Aug 2018

Raw experimental data for 3D structures highlighted at PDBe

PDBe, IRRMC, SBGrid, EMPIAR and BMRB are pleased to announce a web component available on the PDBe web pages that enables users to easily access unprocessed experimental data associated with PDB structures.

PDBe-KB collates functional annotations and predictions for structure data in the PDB archive

30 Jul 2018

PDBe-KB: Help us enrich protein data with functional annotations

PDBe is looking for feedback on a new resource, PDBe-KB (Protein Data Bank in Europe - Knowledge Base), a community-driven resource managed by the PDBe team, collating functional annotations and predictions for structure data in the PDB archive. PDBe-KB is a collaborative effort between PDBe and a diverse group of bioinformatics resources and research teams across the world.

PDB Art exhibition 2018

19 Jul 2018

Celebrating Art Inspired by the PDB

Over the past couple of years, PDBe has worked with local arts societies and schools, using protein structures to inspire artworks. Today, that work is celebrated and shared in a public exhibition of this work at the Michaelhouse Cafe in Cambridge.

UKSR50 poster prize winner 2018

29 Jun 2018

Poster prize awarded at UKSR50 conference

Congratulations to Chai Gopalasingam who won the PDBe poster prize at the UKSR50 conference in Liverpool, UK - celebrating 50 years of Synchrotron Radiation in the UK. Chai, from University of Liverpool, presented a poster titled 'Characterising a bacterial nitric oxide detoxification complex via X-ray crystallography and Cryo Electron microscopy'

He is pictured here with his winning poster.

wwPDB news item image

27 Jun 2018

wwPDB news: ORCIDs To Become Mandatory for OneDep Contact Authors

The wwPDB is making an important change to the data we collect from users at deposition in the OneDep system. Please see the following announcement from the wwPDB:

"The wwPDB OneDep system for deposition, validation and biocuration will require contact authors to provide their unique ORCID identifiers when preparing depositions later this summer. This change will enable wwPDB efforts to correctly attribute PDB structures to contact authors. At a later point, ORCID will be used to authenticate and reorganize access to deposition data within OneDep."

Image of cofactor bound to protein

25 Jun 2018

Spotting Cofactors in the PDB

Cofactors are an essential class of non-protein organic molecules. Among the many small molecules in the PDB archive, they’re now easier to identify.

Many enzymes can’t function without the presence of other, non-protein, molecules known as cofactors (or coenzymes). PDBe and Prof. Janet Thornton’s groups at EMBL-EBI have worked to annotate cofactors and cofactor-like molecules within the PDB archive, building on the Thornton group’s work in the CoFactor database.

PDBe poster prize winner

13 Jun 2018

PDBe poster prize awarded at ENBIK

Congratulations to Jaroslav Budi who won the PDBe poster prize at the recent ENBIK conference in the Czech Republic. Jaroslav, from Comenius University in Bratislava, presented a poster titled 'Dante - genotyping of complex and expanded short tandem repetitions'

He is pictured here receiving the prize from PDBe's Lukas Pravda (on the right).

Image to highlight the EM search improvements at PDBe

05 Jun 2018

Finding detail in the (EM) data

Cryo-electron microscopy (cryoEM) is a field that has made dramatic advances in recent years. This has resulted in many more PDB models, derived directly from electron microscopy data, being released in recent years, therefore it is increasingly important to provide tools for searching and analysing this data.