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TargetDB: A Target Registration Database for Structural Genomics. John Westbrook, Li Chen, and Helen M. Berman, Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Dept of Chemistry and Chemical Biology, Rutgers State University of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854-8087 USA.

TargetDB (http://targetdb.pdb.org/) is a centralized target registration database for sequences from worldwide structural genomics projects that was developed by the Protein Data Bank. Target sequences are collected weekly from the P50 NIH structural genomics centers and other international projects (see http://www.rcsb.org/pdb/strucgen.html). These target sequences are loaded into a relational database, along with the sequences from experimentally determined structures in the PDB and the sequences approved for pre-release by PDB depositors.

Target data are organized by a set of status states that span the details of protein production, structure solution, and the ultimate deposition of experimental and structure data at the PDB. All target data are provided in XML format following recommendations from the International Task Force on Target Tracking(1). All or subsets of these sequence data may be searched using the FASTA sequence comparison method(2). A simple search form is provided to permit queries of each target data element, including: contributing site, protein name, sequence, project tracking identifier, date of last modification, current status of the target, and source organism.

The PDB is supported by funds from the NSF, the DOE, and two units of the NIH: the NIGMS and the NLM.

1. Task Force on Target Tracking. (2001). Task Force Reports from the Second International Structural Genomics Meeting. Technical Report.

2. Pearson, W. R. & Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. U.S.A. 24, 2444-2448.