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Introduction to the Protein Data Bank

The Protein Data Bank (PDB) is an essential resource for accessing experimentally determined 3D structural data of biological macromolecules, obtained via X-ray crystallography, NMR, and electron microscopy. The RCSB PDB portal allows users to search, visualize, and analyze molecular structures, access detailed experimental data, and explore related biological resources. Understanding PDB entries can unveil insights into molecular functions, facilitate drug design, and enhance research in structural biology. For tutorials and resources, visit the RCSB PDB website.

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Introduction to the Protein Data Bank

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  1. Introduction to the Protein Data Bank Learning to Use the RCSB PDB Portal

  2. What is the PDB? • Archive of experimentally determined (X-ray crystallography, NMR, electron microscopy) 3D structural data • It contains • Coordinates of all atoms in the structure • Macromolecular sequences, experimental details and links to other biological resources and databases • Experimental data files used to determine the structures • PDB entries have unique alphanumeric IDs (e.g. PDB ID 1ABC)

  3. Why bother with the PDB? • Visualize the molecule (or parts of it) • Clues to function • Compare and analyze structure • Understand normal functioning and disease states • Design/develop new medicine (diagnostic procedures, treatments)

  4. The Data Pipeline Isolation, Expression, Purification, Crystallization Genomic Based Target Selection Data Collection Structure Determination PDB Deposition & Release 3D Models Annotations Publications

  5. 1 2 3 4 1 2 3 4 The Protein Data Bank

  6. RCSB PDB portal (www.pdb.org)

  7. Using the RCSB PDB website • Searchfor entry (by ID, name, keyword, author, sequence, ligand etc.) • Browse(by source organism, structure classification, biological process, function etc.) • Identify details of a structure • Visualizestructures • Downloaddata files for analysis and use • Create reports(tabular, drill down, collage) • Linkto various other resources (e.g. PubMed, UniProt, SCOP, CATH, GO etc.)

  8. Searching

  9. Browsing

  10. Exploring a Structure

  11. Widgets

  12. Visualization Options • Context-sensitive 3D Viewers • Asymmetric unit • Biological assembly • Biological assembly displayed by default • For X-ray structures: presumed oligomeric state displayed

  13. Sequence Interactive 3D Views of Domain Annotations

  14. Poseview Exploring Ligand Environments

  15. Query Results Browser

  16. Query Refinements

  17. Tabular Reports

  18. Image Collage

  19. MyPDB Keep up-to-date with new structures Framework to store user preferences Saves queries in a private account Notifies users via email when new structures match stored queries

  20. Resources/Tutorials • Collection of tutorials: http://www.rcsb.org/pdb/static.do?p=education_discussion/educational_resources/index.html#tutorials • Getting started:http://www.rcsb.org/pdb/static.do?p=general_information/getting_started/index.html • Screencasts: http://www.rcsb.org/pdb/static.do?p=general_information/screencasts.jsp • Openhelix tutorial: http://www.openhelix.com/pdb • Help: http://www.rcsb.org/pdb/staticHelp.do?p=help/index.html

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