Sure ... If you start searching for protein-DNA docking procedures you
should some way to start ...
You could maybe start with this recent paper ... References in the paper
should also be useful
http://nar.oxfordjournals.org/content/early/2015/05/14/nar.gkv493.full
Ideally you would use different docking methods and come to the same
result ... Plus validation (ideally some sort experimental validation)
may be needed ....
But again, the situation changes and becomes significantly more easy if
your protein has a known type of fold for which structures of complexes
with DNA exist ...
Best
Vlad
On 02/25/2016 04:08 PM, Mahdieh Hadi wrote:
> I have a dna sequence and my protein structure. I do not have the complex structure of them. And I am going to investigate the binding energy between non mutated Dna and protein. Then I am going to do the same for Dna sequence with different mutations to find the mutations which will destroy the interactions completely.
> But, I think that a low quality docking will destroy all of my predictions and at first I should find the best approach for docking.
> Bests!
> ________________________________________
> From: Vlad Cojocaru [vlad.cojocaru.mpi-muenster.mpg.de]
> Sent: Thursday, February 25, 2016 4:04 PM
> To: Mahdieh Hadi
> Subject: Re: [AMBER] Question regarding protein-Dna binding free energy
>
> Well. what do you mean by superposition ?? As far I understand your
> question, you actually need to dock them first, validate your results
> from the docking before you can say you have a reliable complex
> structure. Of course if protein has homologs for which a structure with
> DNA is available, homology modeling may be enough .... Hard to say
> what you actually need from your description ...
>
> Vlad
>
> On 02/25/2016 03:56 PM, Mahdieh Hadi wrote:
>> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> --
>> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> --
> 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
>
--
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 - 07:30:04 PST
