Data Exploration Services

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

Fast and accurate search of protein structures by 3-dimensional shape in large databases continues to be a challenge in Bioinformatics. This has been exacerbated by the recent appearance of accurate methods to predict protein structures from sequence. Those methods, when applied to existing protein sequence databases, produce numbers of structures many orders of magnitude larger than the existing experimental knowledge in the PDB database. The incumbent will research novel methods to compare macromolecular structures that are scalable to the deluge of structural data and that work at any level: domains, chains or assemblies. The ultimate aim of this project is to improve the findability of data in the PDB by building the next generation search engine for structural molecular biology.

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

Going to ISMB? Let us know and RCSB PDB members can discuss this position with you at the meeting.

RCSB PDB longer serves PDB data in the MMTF compression format as of July 2, 2024. Users are strongly encouraged to switch to accessing the data files offered in the compressed BinaryCIF (BCIF) format.

The MMTF compression format for PDB coordinate data was introduced in 2016 for storing macromolecular 3D coordinate data. Since 2020, the BinaryCIF format has been used by RCSB PDB as the preferred compression data format.

BinaryCIF (BCIF, GitHub) stores text-based CIF files using a more efficient binary encoding. It enables both lossless and lossy compression of the original CIF file.

NGL has been removed as a molecular viewer option from RCSB.org Structure Summary Pages (Structure tab) as of June 28, 2024. We recommend users to fully transition to using Mol* for 3D visualization. Mol* offers enhanced features and improved performance for visualization needs.

A comprehensive migration guide can help facilitate a smooth transition from NGL to Mol*.

Extensive Mol* documentation is available and is searchable from the top RCSB.org search box. This search tool is available to quickly find answers to questions related to this migration process and for Mol* feature exploration.

In fall of 2024, electron density map coefficients will be available in the public PDB archive for all X-ray structures. These map coefficients will be the same as used in wwPDB Validation Reports.
The new map coefficients files will replace the electron density maps and combined map coefficient files distributed by RCSB PDB and used by the NGLviewer at RCSB.org. These data (currently served by EDMAPS.rcsb.org) are calculated using publicly-available coordinate files and structure factor files and offered in DSN6 formatted map files and MTZ formatted map coefficient files. With the shutdown of the NGL viewer, the data served by EDMAPS.rcsb.org are no longer needed to run the RCSB PDB website.
RCSB PDB will be phasing out EDMAPS.rcsb.org:

1. June 28, 2024: DSN6-formatted map files will no longer be provided. EDMAPS.rcsb.org will only serve MTZ files with map coefficients.
2. Fall 2024: Electron density map coefficients will be available in the public PDB archive for all X-ray structures. At this point, EDMAPS.rcsb.org will be shut down, including access to MTZ files with map coefficients from this service.

Please contact info@rcsb.org with any questions about this transition.