[Molvis-list] Additional questions

Eric Martz emartz at microbio.umass.edu
Fri Nov 19 14:36:40 EST 2004

At 11/18/04, H.Iiduka wrote:
>1.How to detect monomer-monomer interactions, H-bonds, hydrophobic
>   interactions and electrostatic interactions etc. And Which visualization-
>   tool is best for visualizing them?

The "best" is a matter of personal preference. A very easy to use, yet 
powerful tool is Protein Explorer (proteinexplorer.org, which is largely my 
own work). Noncovalent interactions between any selected moiety and the 
remainder of the PDB file are displayed in a few clicks at the QuickViews 
control panel: SELECT (moiety), DISPLAY Contacts (try both options).

QuickViews also has one-click displays of cation-pi interactions and salt 

>2.Are there any tools to predict quaternary structures and it's interaction
>   sites from tertiary structures?

The Probable Quaternary Structures (PQS) site at EBI is a very good one for 
crystallographically-determined tertiary structures.
You can access it in Protein Explorer: click on "PE Site Map" (near the 
Zoom button in QuickViews), then External Resources.

PQS offers you the coordinates for predicted multimers, with links to 
display them directly in Protein Explorer.

Eric Martz, Professor Emeritus, Dept Microbiology
University of Massachusetts, Amherst MA US

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