ADL: Request for help protein protein docking

filip fratev filipfratev at yahoo.com
Wed Feb 22 23:13:28 PST 2012


Or much better HADDOCK


Regards,
Filip



________________________________
 From: shashank rana <shashank.bioinfo at gmail.com>
To: autodock at scripps.edu; Delwar Hossain <hossaind2004 at yahoo.com> 
Sent: Thursday, February 23, 2012 7:37 AM
Subject: Re: ADL: Request for help protein protein docking
 
You have to use HEX for protein protein docking.

Regard
Shashank

On Wed, Feb 22, 2012 at 11:58 PM, Delwar Hossain <hossaind2004 at yahoo.com>wrote:

> Hi autodock user:
>
> I am trying to docking a protein which has residue 32 residues.
> i)                    I make all the bonds non rotatable
> ii)                   I keep the target protein as rigid
> I received the following results which look far away from experimental
> results. Since, I never did protein-protein docking; I am confused with
> these results.
> Experimental Results:
> Kd (μM) 1.30 ± 0.36
>
> ΔH  (kJ/mol -70.46 ± 6.28
>
> ΔG (kJ/mol) -33.64 ± 0.67
>
> ΔS (J/K mol) -123.55 ±22.04
>
> Autodock Results:
> Estimated Free Energy of Binding    = +21.27 kcal/mol       : Is it del G
> value?
> Partition function, Q =    96.47            at Temperature, T = 298.15 K
> Free energy,        A ~ -2707.20 kcal/mol   at Temperature, T = 298.15 K
> Internal energy,    U =    21.28 kcal/mol   at Temperature, T = 298.15 K
> Entropy,            S =     9.15 kcal/mol/K at Temperature, T = 298.15 K
> Before I can get the Ki value from the output. But this time I did not
> found Ki value!!
>
>
> I also try to include solvent. But I did
> not find the option how to include solvents. When I try to add charge,
> it shows me different time different value.
> I use AUTODOCK 4.2
> I therefore, request if some one can help me providing  valuable
> suggestions how I can produce reliable results
> using AUTODOCK.
> I am eagerly waiting for your generous help.
> Thank you.
> With best regard
> Delwar Hossain
> NDSU
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