AMBER Archive (2009)

Subject: Re: [AMBER] Protein Docking

From: Simon Becker (simon.becker_at_uni-konstanz.de)
Date: Tue May 12 2009 - 10:23:02 CDT

Hi Lin,

I had the same problem once, as I wanted to do docking starting from a
x-tal structure. First I did a long equilibration run (~20 ns) without
the ligand and the rmsd value stabilised over time, than steered md
(slowly!) with the ligand. As the ligand entered the binding pocket the
rmsd changed again and stabilised within 2ns of subsequent
equilibration. So I was fairly sure everything was good.

Also you could try:
- analyse the h-bonds
- mm_pbsa of the docking process

hth
simon

steinbrt_at_rci.rutgers.edu schrieb:
> Hi Lin,
>
> if your ligand-protein conformation stays close to its initial value
> during an MD run that's a good indication (but by no means a proof) that
> it is a reasonable complex geometry and good for further study.
>
> I would say that if you can show a stable complex rmsd during a
> multi-nanosecond MD run, you can claim that your previous docking was
> "successful", but there is no way besides some sort of empirical
> verification to check that it also is correct, i.e. a complex geometry
> occuring under physiological conditions.
>
> Kind Regards,
>
> Thomas
>
> On Mon, May 11, 2009 4:21 pm, Chih-Ying Lin wrote:
>
>> HI
>> When i visualize the MD trajectory, the protein and ligand are closed by.
>> But, I don't know if ligand really DOCK on the protein.
>>
>> Please tell me how to define the successful docking.
>> Thank you
>> Lin
>>
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>>
>>
>
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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> 

-- 
Simon Becker
Dept. of Biology
Molecular Bioinformatics
Box M647 
Universitaet Konstanz
D-78457 Konstanz 

mail: simon.becker_at_uni-konstanz.de
Tel: 0049 7531 882900, Fax: 3183

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