VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Wed Jul 01 2009 - 15:59:33 CDT

In Russo & al, Structure, (2006) 14, 1449-1458, the active site of an encephalitis

virus protease ( pdb 2hwk) with no closely analogous structures available, was modeled on

a hydrolase (pdb 1euv) with bound inhibitor by 'superimposing' the residues that form

the catalytic triad. When they did this, they found that the inhibitor made analogous

contacts on 2hwk that appear sensible. There is nothing in the experimental on how

they did this.

 

Can something like this be done with VMD?

 

Thanks!

Irene

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