[Dock-fans] How to read score outputs

Scott Brozell sbrozell at scripps.edu
Fri Aug 15 16:16:21 PDT 2008


Hi,

On Fri, 15 Aug 2008, Francesco Pietra wrote:

> I was unable to trace a punctual description how to read score outputs
> from Dock6. Therefore I am asking advice here, listing the outputs for
> compounds A and (within square graphs [..] B, for docking on the same
> protein. I would like to learn about the units used, the significance
> of the positive or negative sign (does - for the same absolute value -
> negative mean a better score?), and the meaning of the disentangled
> values for each scoring method. Finally, as a check about
> understanding, is A or B better scored?
> 
> RIGID SCORE
> Grid score -23.264351 [-53.718163]
> vdw         -23.512535 [-53.544125]
> es              0.248185   [-0.174037]
> 
> 
> FLEX SCORE
> Grid score -62.712553 [-66.108734]
> vdw          -62.230541 [-65.598976]
> es              -0.482013   [-0.509760]

DOCK uses lengths in angstroms, masses in atomic mass units,
charges in electron charges units, and energies in kcal/mol.

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#GridEnergyScoring
...
scores are approximate molecular mechanics interaction energies, consisting of van der Waals and electrostatic components
...

> AMBER SCORE LIGAND
> Amberscore 17266.648438      [48.860210]
> complex        8923.085840 [-8288.038497]
> receptor        8393.643253   [8393.643253]
> ligand             -50.079834      [-56.744643]
> 
> 
> AMBER SCORE EVERYTHING
> Amberscore -83.733109       [-72.851837]
> complex -13975.261923 [-13957.715947]
> receptor  13941.608651 [13941.608651]
> ligand         -50.079834        [-56.744543]

Amber score uses lengths in angstroms, masses in atomic mass units,
charges in electron charges units, and energies in kcal/mol
(as is done in Amber).
Internally and on input of charges for amber score from a prmtop file
the charges are scaled by 18.2223; see 
http://amber.scripps.edu/Questions/units.html

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScore
...
The AMBER score is calculated as:
E(Complex) - [ E(Receptor) + E(Ligand) ],
where E(Complex), E(Receptor), and E(Ligand) are, respectively, the internal energies of the complex, receptor, and ligand (all solvated) as approximated by the AMBER force field with a GB/SA solvation term.
...
The AMBER score output in the DOCK output contains energy terms for each species (complex, receptor, and ligand) such that the sum of the terms is equal to the score; in particular, note that the receptor and ligand values have been negated. 


So Amber score energies are differences of complete MM energies.
http://amber.scripps.edu/eqn.txt
And DOCK score energies are MM interaction energies.
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#GridEnergyScoring
(All this ignoring solvation which Amber score and some DOCK scores
include.)
All scores can be considered as approximate binding energies, but see
my usual comment on the often unmentioned scale of the approximations:
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-March/000973.html

Thus, B gets the gold even though A won one heat closely
(AMBER SCORE EVERYTHING).

Scott




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