[Dock-fans] How to read score outputs

Francesco Pietra chiendarret at gmail.com
Fri Aug 15 07:26:32 PDT 2008


Hi:
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]


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]


Thanks
francesco pietra


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