Protein Data Bank (PDB)

The Protein Data Bank (PDB) is an international repository and the primary source for information about the structure of biological macromolecules. The PDB is a key research resource that is essential for our understanding of living systems. It serves a broad community of experimental, structural, and computational scientists and educators at all levels. PDB access is provided through primary web and ftp sites (www.pdb.org, ftp.pdb.org) or via multiple mirror sites distributed worldwide. The PDB is managed by the Research Collaboratory for Structural Biology (RCSB), consisting of a partnership between Rutgers, the University of California San Diego and the Scripps Institute of Oceanography to provide a single, searchable archive of accurate and well-annotated data on experimentally determined macromolecular structure. Systems developed by RCSB are currently being used for data processing, archiving, distribution and query, as well as maintenance of the physical archive. In addition to continued operation of the primary data archiving, ingestion, and dissemination functions, the project is implementing several enhancements to the infrastructure associated with the two main operational functions of the archive: data ingestion and processing, and data dissemination. Improvements include provisioning of a robust, high-throughput pipeline to manage ongoing increases in the volume and complexity of data submitted to PDB, development of query, analysis, visualization, and reporting tools to enhance access to PDB data, and development of a range of education and outreach activities that support the use of PDB data by teachers and students at all educational stages. The result of this effort is a significant improvement in the utility and value of the Protein Data Bank for both specialists and non-specialists alike. 

Mechanisms for increasing the broader impacts of this work include the following: a series of workshops and meeting sessions, active participation in scientific meetings, a regular newsletter, the on-going use of a help desk to increase the access and utility of PDB for the specialist and non-specialist research community, and use of focus groups to insure maximum usability of PDB data. Participation in graduate and undergraduate coursework design and implementation and in structured research opportunities is being used to increase the impact of PDB on university-level education. Participation in teacher training workshops and a collaborative effort to launch a teacher development program provide opportunities to bring PDB resources to the K/12 environment. The general public is being made aware of PDB efforts through a traveling art exhibit and through frequent news releases and informational programs. Online-based activities like the “Structural View of Biology” and “Molecule of the Month” will reach audiences nationally and globally. New activities to be introduced under the current award include increased outreach to under-represented communities and the development of annual theme topics to provide a focus for national integration of education activities involving structural biology. Collectively, these efforts will extend the benefits of PDB resources and activities to the broadest possible community. More information can be found at the PDB website (https://www.rcsb.org/).