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PDB Data Assembly and Validation Tools. John Westbrook, Zukang Feng, Huanwang Yang and Helen M. Berman. PDB, RCSB, Dept. of Chemistry and Chemical Biology, Rutgers, The State Univ. of New Jersey, 610 Taylor Rd., Piscataway, NJ 08854.

The Protein Data Bank has developed a suite of software tools to assist structural biologists in the automated assembly and validation of structure depositions.

The automated assembly of PDB structure depositions is greatly facilitated by the PDB_EXTRACT program. This software tool processes the output files produced by most structure determination applications and extracts the data items required for deposition. Information from data collection to final refinement can be automatically merged into an mmCIF file. Little additional manual effort is required to complete a deposition.

PDB validation tools support the recommendations of the International Structural Genomics Organization (ISGO) Task Force on Numerical Criteria for Evaluating and Assuring Structure Quality (2001, http://www.nigms.nih.gov/news/reports/airlie_tasks.html). Validation reports can be created through the PDB web deposition system (ADIT, http://deposit.pdb.org/adit/) or by using standalone tools. PDB validation reports are electronically packaged such that they may conveniently accompany a manuscript through the peer review process.

The software described in this talk is available under an Open Source license at http://deposit.pdb.org/software/.

The Protein Data Bank (PDB; http://www.pdb.org/) is operated by Rutgers, The State University of New Jersey; the San Diego Supercomputer Center at the University of California, San Diego; and the National Institute of Standards and Technology – three members of the Research Collaboratory for Structural Bioinformatics (RCSB). The PDB is supported by funds from the NSF, the DOE, and two units of the NIH: the NIGMS and the NLM.