Newsletter | Summer 2016 ⋅ Number 70

Data Query, Reporting, and Access

Month Unique Visitors Visits Bandwidth
April 2016 378,006 871,085 3679.44 GB
May 2016 356,342 844,134 3379.94 GB
June 2016 326,771 802,741 3186.85 GB

3D view of L-Cystine modification in entry PDB ID 4V1J.

Two new features have been recently added to rcsb.org:

Protein Modifications in the PDB have been mapped to the RESID database of Protein Modifications and the associated Protein Modifications Ontology (PSI-MOD).  Explore these modifications with the new Protein Modification Browser, Advanced Search, and the 3D View and Sequence options on Structure Summary pages. A detailed overview is available.

Biological assembly files for large structures are now available in PDBx/mmCIF format from Structure Summary pages.   The biological assembly is the macromolecular assembly that has either been shown to be or is believed to be the functional form of the molecule. The PDBx/mmCIF format has no restrictions on the number of atoms and chains and can hold biological assemblies of any size.  For more information, see PDB-101’s biological assembly tutorial.   These data files can be downloaded from each Structure Summary page.

3Validation Summary Slider

In May, wwPDB Validation Reports for all Nuclear Magnetic Resonance (NMR) and 3D Cryo Electron Microscopy (3DEM) structures already represented in the global PDB archive were publicly released. 

RCSB PDB prominently displays the Validation Summary Slider graphic at the top of all Structure Summary pages and links to the full report PDF.

wwPDB Validation Reports assess the quality of each structure and highlight specific concerns, by examining the coordinates of the atomic model derived from either NMR and 3DEM, and by comparing the coordinates of the atomic model derived from NMR with primary experimental data therefrom. Readily interpretable summary information compares the quality of the atomic model with structural models from across the entire archive, thereby helping users of PDB data critically evaluate the quality of each archival entry.

These new validation reports implement recommendations provided by NMR and 3DEM community experts on validation, while reusing elements of the validation schema developed for structures determined by X-ray crystallography.



We are looking for a talented and highly motivated Postdoctoral Fellow to join our multidisciplinary team at UC San Diego.

The Challenge: Develop innovative analysis, integration, query, and visualization tools for 3D biomolecular structures to help accelerate research and training in biology, medicine, and related disciplines. In this project, we will employ the latest advances in computer science to develop highly interactive features and scalable services and workflows for the RCSB PDB website.

This position is a unique opportunity to engage in leading edge research, development, and outreach activities of the RCSB PDB with worldwide impact.

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Structural Bioinformatics, or related field with a focus on software development
Structural Biology with a focus on software development
Computer Science with a focus on bioinformatics algorithm development or visualization

Demonstrated proficiency in a high-level programming language, such as Java or Python and experience with state of the art software development tools. Experience with front-end programming languages (JavaScript) and libraries. Strong skills in problem solving and algorithm design are required. High productivity demonstrated by publications and contributions to open source software projects. Experience in the development of modern web applications, user interface design, or scientific visualization is a plus. Excellent written and oral communication skills.

Visit our Careers page for more information.

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