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

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introduction to the protein data bank

Introduction to the Protein Data Bank

Learning to Use the RCSB PDB Portal

what is the pdb
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)
why bother with the pdb
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)
the data pipeline
The Data Pipeline

Isolation,

Expression,

Purification,

Crystallization

Genomic

Based Target

Selection

Data

Collection

Structure

Determination

PDB Deposition

& Release

3D Models

Annotations

Publications

using the rcsb pdb website
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.)
slide12

Visualization Options

  • Context-sensitive 3D Viewers
    • Asymmetric unit
    • Biological assembly
  • Biological assembly displayed by default
  • For X-ray structures: presumed oligomeric state displayed
sequence
Sequence

Interactive 3D

Views of

Domain Annotations

mypdb
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

resources tutorials
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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