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The Protein Data Bank and the Nucleic Acid Database

The Protein Data Bank and the Nucleic Acid Database. Chemistry 537 October 23 and 28, 2002 Helen M. Berman. http://www.pdb.org/. Data Assembly. Integrity Checking. Structure Validation. Archiving. Distribution And Query. Analysis. History of the PDB. 1957

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The Protein Data Bank and the Nucleic Acid Database

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  1. The Protein Data Bank and the Nucleic Acid Database Chemistry 537 October 23 and 28, 2002 Helen M. Berman

  2. http://www.pdb.org/

  3. Data Assembly Integrity Checking Structure Validation Archiving Distribution And Query Analysis

  4. History of the PDB 1957 • Myoglobin structure determined 1970s • Community discussions about how to establish an archive of protein structures • Cold Spring Harbor meeting in protein crystallography • PDB established at Brookhaven (October 1971; 7 structures) 1980s • Number of structures increases as technology improves • Community discussions about requiring depositions • IUCr guidelines established • Number of structures deposited increases • Independent biological databases established – e.g., the NDB 1990s • mmCIF project completed • Structural genomics begins • PDB moves to RCSB

  5. Cold Spring Harbor Symposia on Quantitative Biology, vol. XXXVI, 1972

  6. Year 2001 Demographics of Depositions Geographic Region 58% - North America 26% - Europe 13% - Asia 2% - Australia/New Zealand 0.3% - South America Release Status 71% - HPUB 17% - REL 12% - HOLD Macromolecule Type 90% - Protein 6% - Nucleic acid 4% - Protein/Nucleic acid complexes Experimental Method 80.6% - X-Ray diffraction 16.2% - NMR 2.7% - Model 0.4% - Electron diffraction 0.1% - Neutron diffraction

  7. PDB Growth

  8. New Folds as a % of Total PDB Depositions

  9. Validate PDB ID PDB Entry Archival Data Distribution Site Core DB Corrections Data Processing Data Flow Step 2 Validation Report Step 1 Depositor Annotate ADIT Step 3 Step 4 Depositor Approval Step 5 Functional Annotation

  10. Integrated Data Processing System

  11. Integrated Query System WWW User Interface SearchFields SearchLite Query Result Browser Structure Explorer New queries New queries New tools New tools DB INTEGRATION LAYER FLAT FILES KEYWORDSEARCH DERIVED DATA CORE DB BMCD FTP tree (download) CORBA Interface Remote Applications

  12. http://ndbserver.rutgers.edu/

  13. History • 1976-89 Informal archive • 1990 NDB established with NSF funding • 1992 Processed files for PDB • 1996 Official deposition site • 1998 Founding member of the RCSB New manager of the PDB • 2002 Launch of the new NDB

  14. New Home Page

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