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Using the Protein Data Bank: An RCSB-PDB tutorial and more

Using the Protein Data Bank: An RCSB-PDB tutorial and more. Shuchismita Dutta September 2006. The Protein Data Bank. Archive 3-D structural coordinates Experimental data Free wwPDB RCSB, PDBj, EBI-MSD, BMRB. Data files 3-D Coordinates Experimental data. Website

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Using the Protein Data Bank: An RCSB-PDB tutorial and more

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  1. Using the Protein Data Bank:An RCSB-PDB tutorial and more Shuchismita Dutta September 2006

  2. The Protein Data Bank • Archive • 3-D structural coordinates • Experimental data • Free • wwPDB • RCSB, PDBj, EBI-MSD, BMRB

  3. Data files 3-D Coordinates Experimental data Website Query (Search/Browse) Links Data analysis Visualization RCSB-PDB

  4. Header: The who, what, where, why, when, how about the structure Coordinates: The x, y, z, occupancy etc. for each atom Experimental Data: Structure factor file (X-ray) Constraint file (NMR) EM map or volume (EM) Data files

  5. Navigating

  6. Searching & Browsing

  7. Structure Summary & Queries

  8. Links & Analysis

  9. PDBsum

  10. PDB related resources

  11. Graphics KiNG WebMol Jmol Protein Explorer Default image

  12. … and More … • NDB • Where do I find … • PDB resources • NCBI resources • EMBL-EBI resources

  13. The Nucleic Acid Database (NDB)

  14. Atlas pages

  15. NCBI resources

  16. EMBL-EBI resources

  17. Where do I find … • Sequence, Name: GenBank, UniProt • Source organism: Taxonomy • Cellular location: GO • Secondary structure: SCOP, CATH • 3D structure: PDB and related resources • Biologically relevant structure or assembly: PDB,PQS • Biological function: GO, PubMed, ENZYME • PDB, NCBI, EMBL-EBI related resources

  18. Should I believe this …? • Source • Authors • Evidence • Experiment • Controls • Conclusion and Discussion

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