News

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.

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).

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