The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema - PubMed (original) (raw)

. 2005 Jan 1;33(Database issue):D233-7.

doi: 10.1093/nar/gki057.

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. 2005.

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.

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