ADL: Request for help protein protein docking

Delwar Hossain hossaind2004 at yahoo.com
Wed Feb 22 10:28:35 PST 2012


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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