ADL: Here is the reason for energy difference..

Savani Anbalagan savani1987 at
Tue Oct 30 04:00:53 PDT 2007


@ Daniel:
I guess that might not be the reason.. cos only if we are going to follow
all the steps for performing flexible docking then there might be the

in this case same steps follwed for autodock3 is done for autodock4..

c from autodock site i got these... hope it answers y such an energy

it says

AutoDock 4.0 now has a free-energy scoring function that is based on a
linear regression analysis, the AMBER force field, and an even larger set of
diverse protein-ligand complexes with known inhibiton constants than we used
in AutoDock 3.0.

AutoDock 4 computes the unbound state of the ligand before docking as an
extended conformation, and includes the difference in internal interaction
energy between this unbound state and the final docked state, when
estimating the free energy of binding. Previously, AutoDock (guess they mean
Autodock 3.0) assumed that the internal energy of the ligand was the same
both before and after binding to the macromolecule.

AutoDock 4 uses a more reasonable distance for the non-bond cutoff in the
internal energy calculations, which speeds up docking compared to

The internal energy calculation now includes the desolvation energy term.
Previously, AutoDock 3 only used the desolvation energy term in the
intermolecular interaction energy.

The internal energy calculation now uses the same distance-dependent
dielectric function that is used in the intermolecular interaction energy
calculation. Previously, AutoDock 3 only used the distance-dependent
dielectric function in the intermolecular interaction energy.

The desolvation term in AutoDock 4 now supports more atom types than the
Stouten method implemented in AutoDock 3, which is particularly useful in It
now includes the absolute magnitude of an atom's partial atomic charge to
evaluate its contribution to the total desolvation free energy.

Anyway Lanny has got lesser energy by Autodock4.. there v r in safer side..

With Regards,

Savani Anbalagan

From: "Daniel Jana" <dfjana at>
Subject: Re: ADL: docking energy difference between autodock3 and
To: autodock at
       <42156b9d0710290330o2630a5pf2e905d41cba8889 at>
Content-Type: text/plain; charset=ISO-8859-1


According to an email sent by Anurag in the 16th of October:

"With reference to your queries on the Autodock archieves, the main
difference between autodocks' versions 3 and 4 is that 3 takes into account
only the ligand flexibility where as version 4 also considers the side-chain
flexibility of the receptor molecule."

Hope this helps!


Take Care,
Savani Anbalagan

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