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Slide List for This Module
Structures: Title slide/table of contents
Background:
Four Levels of Structure
Lab Techniques: How are Structures Resolved?
NMR and X-Ray Crystallography: Examples
Protein Data Bank (PDB)
Structure Record Format: PDB
Molecular Modeling Database (MMDB)
Structure Record Format: ASN.1
3-Dimensional View of Structure Record
Searching for Structures
Fewer Structures than Protein Sequences
"Front Doors" and "Back Doors" for Retrieving Structures
Using Front Door #1 (Search for P53 Tumor Suppressor Protein)
Using Front Door #2 (Link from P53 Tumor Suppressor Protein Sequence Records to Structure Record)
Understanding the Output: Structure Record Summary
Cn3D ("See in 3-D") Viewing Software
Installing Cn3D
Viewing the 3-Dimensional Structure
Two Types of Related Records for Structures
Using the Back Doors (Finding structures in the absence of an exact query match)
Hands-On
Demonstration Exercise: MLH1
(Finding structures related to the human MLH1 gene product)
Mastery Exercise: PER2
(Finding structures related to the human period (PER2) gene product)
Review of Structure Searching Methods: Examples of Front Doors and Back Doors That We Tried
Additional User Questions
Structure News:
PubChem Project: Small Molecules
PubChem Databases:
PubChem Substance
PubChem Compound
PubChem BioAssay
References
Slide List for This Module
Structures
Revised 11/06/2007
