Subject: Re: CCL:W:Protein-DNA Docking

From: Giulio Vistoli <giulio.vistoli[at]unimi.it>
Date: Wed, 30 Mar 2005 10:19:21 +0200

Dear Noeris Salam,

To perform DNA-protein docking you can try our free EscherNG program 
(www.ddl.unimi.it). It is a parallelized version of Escher algorithm of 
Helmer-Citterich and co-workers, allowing the docking of DNA also.

Best regards

Giulio Vistoli

---

From: "David A. Case" <case~at~scripps.edu>
Date: Wed, 30 Mar 2005 07:30:27 -0800

On Tue, Mar 29, 2005, Noeris, , Salam wrote:
> 
> Can someone please offer advice on available software that can perform
> Protein-DNA docking (free or commercial). Or software that is suited towards
> the study of Protein-DNA binding interactions.
> 

You could look at the following paper:

%A V.A. Roberts
%A D.A. Case
%A V. Tsui
%T Predicting Interactions of Winged-Helix Transcription Factors with DNA
%J Proteins
%V 57
%P 172-187
%D 2004

The "dot" program used there is available at http://www.sdsc.edu/CCMS/DOT/
(although that site seems to be somewhat dated...)

...good luck...dave case