Thanks a lot for your answer. :)
So, I just use amber for investigating interactions between DNA and Protein, if I have their complex. Is it true?
And superimposition of them is not possible by Amber. Yes?
________________________________________
From: Vlad Cojocaru [vlad.cojocaru.mpi-muenster.mpg.de]
Sent: Thursday, February 25, 2016 3:52 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Question regarding protein-Dna binding free energy
Well, you are asking for different entire training sessions by email ...
I guess you realize this is not really possible. Maybe you could start
in searching the literature about how to predict the configuration of
protein-DNA complexes when you don't know the structure (a research
topic on its own) ... Once you have a complex and you are confident in
it (validation very important), you may attempt rough predictions of
base-dependent differences in DNA binding affinity (another research
topic on its own, Rosetta software may be an interesting starting point
) .. Or you may want to simulate it with classical MD or advanced
enhanced sampling techniques (other research topics on their own)...
So, probably what you have to do is to read and read and read before you
can start something ....
Vlad
On 02/25/2016 03:25 PM, Mahdieh Hadi wrote:
> Hi,
> I have prepared pdb, inpcrd and prompt files for my DNA, and I have pdb file of my protein. But I do not have the complex of them. I am going to predict the mutations in my DNA sequence that will decrease the binding affinity to the protein to the least level.
> Would you please give me an overview of what should I do? How should I prepare DNA-Protein complex and etc?
> Bests
> Mahdieh
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>
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Thu Feb 25 2016 - 07:00:05 PST
