Okay I have calculated the DOPE scores and I will use these. Just out
of interest, is there are way of utilising the Z scores or compactness
scores from GA341? From the example below I am assuming that the lower
the Z score the better, would this be correct? Also when it comes to
the compactness value is a higher or lower score better?
Many thanks
Jo
model1
% sequence identity : 30.174000
Sequence length : 531
Compactness : 0.270804
Native energy (pair) : -225.273799
Native energy (surface) : -13.946407
Native energy (combined) : -6.357012
Z score (pair) : -9.813731
Z score (surface) : -7.147611
Z score (combined) : -11.464915
GA341 score : 1.000000
model2
% sequence identity : 30.174000
Sequence length : 531
Compactness : 0.256617
Native energy (pair) : -268.422282
Native energy (surface) : -16.727187
Native energy (combined) : -7.618686
Z score (pair) : -9.969647
Z score (surface) : -7.755271
Z score (combined) : -12.156111
GA341 score : 1.000000
jo hanna wrote: > After having built my models, i have decided to assess them using the
> ga341 score.
> the ouput of this script for two different models is: > > model1 >
GA341
score :
1.000000 > > model2 > GA341
score :
1.000000 > > how do i interpret these outputs? should both scores be 1?
GA341 is not sufficiently sensitive to distinguish between two 'very good' models. Any good model will give a score very close to 1 (
e.g. running GA341 on most PDB structures will give a 1.0 score). You should use it only to discard 'bad' models (e.g. those with score less than 0.6). DOPE may be more sensitive in your case.