Subject: structure verification

From: Christian Pilger <[email-masked]>
Date: Thu, 5 Apr 2001 15:21:27 +0200

Dear CCLers,

I ran a series of MD calculations on a protein, partially solvated in
water with the aim to equilibrate the solvent molecules. The equilibrated
structure is going to be employed in a docking study.

I would like to ask for your opinions: is it valuable/necessary to check
such an equilibrated protein structure by means of tools available for
structure verification in macromulecular Xray crystalography/NMR
spectroscopy, such as WHATIF and/or ADIT from the PDB ? Are there other
programs available for this type of validation ?

Ciao,

Christian

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 Dr. Christian Pilger 

    Istituto di Strutturistica Chimica "Giordano Giacomello"
    C.N.R. - Sezione di Trieste
    Area Science Park - Basovizza
    Strada Statale 14 - Km. 163.5
    I-34012 Trieste/Italy

   Tel.: +39+040+226881
   Fax : +39+040+9221126
 e-mail: [email-masked]
 
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From: Don Gregory <[email-masked]>
Date: Thu, 05 Apr 2001 08:49:07 -0700

For protein-model verification, we
highly recommended Profiles-3D from Eisenberg's lab at UCLA.

http://www.doe-mbi.ucla.edu/Services/Verify_3D/
http://www.doe-mbi.ucla.edu/Services/
http://www.msi.com/life/products/insight/modules/Profiles-3D_page.html

Don Gregory