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. 2005 Jan 1;33(Database issue):D233-7.
doi: 10.1093/nar/gki057.

The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema

Nita Deshpande  1 , Kenneth J Addess, Wolfgang F Bluhm, Jeffrey C Merino-Ott, Wayne Townsend-Merino, Qing Zhang, Charlie Knezevich, Lie Xie, Li Chen, Zukang Feng, Rachel Kramer Green, Judith L Flippen-Anderson, John Westbrook, Helen M Berman, Philip E Bourne
Affiliations

The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema

Nita Deshpande et al. Nucleic Acids Res. .

Abstract

The Protein Data Bank (PDB) is the central worldwide repository for three-dimensional (3D) structure data of biological macromolecules. The Research Collaboratory for Structural Bioinformatics (RCSB) has completely redesigned its resource for the distribution and query of 3D structure data. The re-engineered site is currently in public beta test at http://pdbbeta.rcsb.org. The new site expands the functionality of the existing site by providing structure data in greater detail and uniformity, improved query and enhanced analysis tools. A new key feature is the integration and searchability of data from over 20 other sources covering genomic, proteomic and disease relationships. The current capabilities of the re-engineered site, which will become the RCSB production site at http://www.pdb.org in late 2005, are described.

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Figures

Figure 1
Figure 1
Primary and secondary references assigned to structures. The primary references are assigned during structure annotation/data curation. Secondary references are collected from external databases using the primary reference identifiers and accession numbers. This is rerun on a weekly basis for new and all existing structures and stored in the database.
Figure 2
Figure 2
Procedure to create structure-OMIM-disease mapping. Disease terms listed in the NCBI book Genes and Disease are used to mine the OMIM text for OMIM numbers associated with the terms. This Disease-OMIM mapping is loaded into the database. Performing a join on the Disease-OMIM table created above and the OMIM-Structure mapping table results in Disease-Structure mapping.
See this image and copyright information in PMC

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