Molecular Structures 2009

Jennifer Lyon, MS, MLIS Eskind Biomedical Library Vanderbilt University Medical Center [email_address]

Introduction ,[object Object],[object Object],[object Object],[object Object],[object Object]

Image from the National Human Genome Research Institute (NHGRI) Talking Glossary of Genetic Terms

Methods ,[object Object],[object Object],[object Object],[object Object]

Understanding X-Ray Crystallography ,[object Object],[object Object],[object Object],[object Object]

Validity – X-Ray Crystallography ,[object Object]

Resolution - Examples ,[object Object]

Understanding NMR Spectroscopy ,[object Object],[object Object],[object Object],[object Object],[object Object]

Summary of Methods X-Ray Provides the highest resolution. Requires crystallization of protein and usually gives only one model of structure. May be automated in future. Reliable resolutions for structures are around 2 angstoms or less. NMR Allows structure determination of protein in solution. Variability of solution conditions possible. Provides characterization of intrinsic protein motion in solution. Computation Simulates the action of the forces that act on each atom in a molecule of known composition and approximates structure. Produces theoretical models. Fast, but presently least reliable.

Databases and Searching ,[object Object],[object Object],[object Object]

The Protein Data Bank ,[object Object],[object Object],[object Object],[object Object]

The PDB Advanced Search ,[object Object],[object Object],[object Object],[object Object]

Viewing Structures From PDB ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Introducing Entrez Structure ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

MMDB (Molecular Modeling DataBase) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Searching Entrez Structure ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Example – Searching ,[object Object],[object Object],[object Object],[object Object],[object Object]

Practice Searching ,[object Object],[object Object],[object Object],[object Object]

Structure Results (DocSum) Click on PDB identifier or photo to see more detailed records Description as provided by author Links to related structures and other related info

MMDB Structure Records ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Comparing PDB and MMDB ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Viewing Structures ,[object Object],[object Object],[object Object]

Introducing Cn3D ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Using Cn3D ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

What Cn3D Does (and Doesn’t) ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

More About Structural Alignments ,[object Object]

VAST – Vector Alignment Search Tool ,[object Object],[object Object]

Why Do Structural Alignments? ,[object Object],[object Object],[object Object],[object Object]

Understanding 3-D Domains ,[object Object]

Identifying 3-D Domains ,[object Object]

Numbering 3-D Domains ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

How Does VAST Work? ,[object Object]

How Does VAST Work? (2) ,[object Object]

How Does VAST Work? (3) ,[object Object]

Let’s Go Live! ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Other Structure Viewers ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Molecular Structures 2009

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Molecular Structures 2009