Image to highlight the search improvements at PDBe

01 Jun 2018

Finding your way with PDBe searches

You might have noticed some changes on the PDBe website recently as we’ve introduced some great improvements to the search options. We hope that these will help you find exactly what you are looking for in the PDB archive. Improvements include the addition of protein sequence searching, many more search terms, an upgraded interface and the ability to input more advanced search queries.

tRNA highlighted within a sea of proteins

29 May 2018

Highlighting RNA in a protein world

We may be called the Protein Data Bank in Europe, but the PDB archive contains more than just proteins. Many PDB entries also contain RNA, and we’ve just made finding them a lot easier.

RNA is vital to life, it carries both the genetic code and amino acids to the ribosome, where the RNA catalyses the synthesis of proteins. But it’s the ‘poor cousin’ to proteins in the PDB, lacking much of the standard naming and classification that proteins enjoy. This makes it difficult to find, for example, all the transfer RNAs.

wwPDB news item image

25 May 2018

wwPDB news: Update to OneDep system

The new version of OneDep improves the process of data replacement for PDB and EMDB entries, prior to their release. This updated process ensures that all new data are checked and validated before the new files are merged into the deposition session. In addition, we are also making sure that we are open and clear about how we handle personal data in OneDep. We have updated the wwPDB privacy policy to comply with the changes brought by the European Union data protection law (GDPR).

Image to highlight the search improvements at PDBe

23 May 2018

Exciting new updates at PDBe

You might have noticed some changes on the PDBe website today as we’ve introduced some great improvements to the search options and new features on our entry pages. All these changes should help you to find what you’re looking for in the PDB archive and give you better biological context for the molecules in your search results.

You’ll notice that the search pages look a little different. This change, consistent with the EMBL-EBI style, means that search results can be viewed more easily across all devices, especially mobiles.

Dr. Liz Blackburn with the David Blow trophy

13 Apr 2018

David Blow Poster Prize awarded at BCA

Congratulations to Dr. Liz Blackburn who was awarded the David Blow poster prize at the recent British Crystallographic Association Spring Meeting.

Image of artwork and the book given to the student as prize

29 Mar 2018

PDBe Explores Art

PDBe recently contributed to an art exhibition in Cambridgeshire celebrating young people's artwork, as part of our ongoing work with school art departments.


wwPDB news item image

28 Mar 2018

Access Updated Validation Reports for PDB Structures

Validation reports for all PDB structures have been updated to include new percentile statistics reflecting the state of the archive on December 31st 2017 and updated versions of third-party software: CCP4/Refmac (7.0 v44), Phenix (1.13) and Mogul (2018) and CSD archive (as539be). The LLDF statistic previously used to identify ligands that do not fit electron density well has been replaced by a combination of Real-space R-factor (RSR>0.4) and Real-space correlation coefficient (RSCC<0.8).

Matthias Barone with the winning poster

27 Mar 2018

Poster Prize awarded at German Crystallographic Society (DGK)

Congratulations to Matthias Barone from Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) who won the PDBe sponsored poster prize at the 26th Annual Meeting of the German Crystallographic Society (DGK) earlier this month.

Matthias is pictured here by his poster "Structure-optimized ProM scaffolds address Ena/VASP as a possible antimetastatic target" with the prize, a copy of Bernhard Rupp's "Biomolecular Crystallography."

Viewing a protein in 3D on a tablet device

15 Mar 2018

Tools for teaching in 3D

Molecular structure, especially biomolecule structure, is tricky to visualise. New resources, produced by Dr Peter Hoare and students at Newcastle University in conjunction with PDBe, help students see in 3D and contextualise their knowledge at the chemistry–biology interface.

Poster prize awardee

10 Mar 2018

VIB Applied Bioinformatics Poster Prize awarded

Congratulations to Gaspar Pinto from Masaryk University who has won the PDBe sponsored poster prize at the VIB Applied Bioinformatics in Life Sciences Conference held 8-9th March in Leuven Belgium. His poster described the software CaverDock, which analyses protein tunnels.

Gaspar (right) is pictured here receiving the prize from Alexander Botzki from VIB Bioinformatics Core