Under the sponsorship of the NIGMS, the PDB has created a centralized registration database for target sequences from the NIH P50 structural genomics projects at http://targetdb.pdb.org/.
Target sequences and status information are collected weekly from the originally funded NIH structural genomics centers: the Berkeley Structural Genomics Center, the Joint Center for Structural Genomics, the Midwest Center for Structural Genomics, the Northeast Structural Genomics Consortium, the New York Structural Genomics Research Consortium, the Southeast Collaboratory for Structural Genomics, and the Tuberculosis Structural Genomics Consortium. The new P50 centers (the Center for Eukaryotic Structural Genomics and the Structural Genomics of Pathogenic Protozoa Consortium) will be added in the near future.
The target database can be searched by sequence using FASTA (Pearson, W.R. and Lipman, D.J. (1988) "Improved tools for biological sequence comparison" PNAS 85:2444-2448). Sequence searches may include only the P50 target sequences or the P50 and PDB sequences. Target sequences may also be searched by contributing P50 site, protein name, project tracking identifier, date of last modification, and the current status of the target (e.g. cloned, expressed, crystallized, ...). Search results may be viewed as HTML reports, FASTA data files, or in XML.
Target data for all of the NIH projects can be downloaded as an XML document. The XML document is organized following the recommendations of the International Task Forces on Target Tracking (see http://www.nigms.nih.gov/news/meetings/airlie.html for more information). This document type definition for the target data file can be retrieved from http://targetdb.pdb.org/apps/target.dtd.
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
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