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RCSB PDB Newsletter | Fall 2013 ⋅ Number 59

Data Deposition and Annotation

Deposition Statistics

In the second quarter of 2013, 2731 experimentally-determined structure entries (coordinates and experimental data) and 132 3DEM maps were deposited to the archive. 8111 coordinate entries and 404 3DEM maps have been deposited in the archive in 2013.

For the entries deposited this quarter, 84% were deposited with a release status of hold until publication; 13% were released as soon as annotation of the entry was complete; and 3% were held until a particular date. 92% of these entries were determined by X-ray crystallographic methods; 5% were determined by NMR methods.

During the same period, 2424 structures were released in the PDB.

NMR Validation Task Force Recommendations Published

We are pleased to announce that the recommendations of the wwPDB NMR Validation Task Force (VTF) have been published:

Recommendations of the wwPDB NMR Validation Task Force Gaetano T. Montelione, Michael Nilges, Ad Bax, Peter Güntert, Torsten Herrmann, Jane S. Richardson, Charles D. Schwieters, Wim F. Vranken, Geerten W. Vuister, David S. Wishart, Helen M. Berman, Gerard J. Kleywegt, John L. Markley Structure (2013) 21: 1563-1570 doi: 10.1016/j.str.2013.07.021
As the number of structures in the PDB determined using NMR continues to grow, the provision of robust validation tools is becoming increasingly important. Assessing the quality of NMR structures and underlying experimental data is a critical area of NMR methods development, and also an essential component of the process of making NMR structures accessible and useful to the wider scientific community.

The wwPDB partners are actively driving the development of new standards and software for the validation of structures determined by NMR spectroscopy. A wwPDB NMR VTF comprised of experts in the field has been convened to define standard validation criteria, representing community consensus. The VTF has provided its initial recommendations, which will be implemented in a wwPDB validation pipeline and applied to all depositions of NMR structures.

This paper summarizes the recommendations of the NMR VTF, and lays the groundwork for future work in developing standards and metrics for biomolecular NMR structure and data quality assessment.

Update: New wwPDB Deposition & Annotation System

Lead annotator Jasmine Young
has used the new system to annotate
new entries.

The wwPDB partners have joined forces in creating the next generation of PDB deposition and annotation tools. The new deposition interface supports structures of any size, determined using X-ray diffraction, EM and/or NMR methods. Community testing is ongoing at the wwPDB partner sites and will be expanded through 2013. The new system will go into full production in early 2014.

The new deposition and annotation tools are designed to ensure an increasingly high quality and dependable resource that will effectively support the anticipated increase in deposition throughput as well as the increase in complexity and experimental variety of submissions over the next 10 years.

Visit wwpdb.org for more information.

Paper Published

How Community Has Shaped the Protein Data Bank Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley Structure (2013) 21: 1485-1491 doi: 10.1016/j.str.2013.07.010.