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. Author manuscript; available in PMC: 2012 Sep 11.
Published in final edited form as: J Med Chem. 2010 Nov 11;53(21):7573–7586. doi: 10.1021/jm100600y

Table 3.

Comparison between different kNN-Dragon QSAR models generated with or without variable selection.

Model Num. Modelsa Confusion Matrix
 Statistics for the Models
N(1)b N(0)c TP TN FP FN SE SP En(1) En(0) CCRevsd Coveragee
Af 908 26 34 20 23 11 6 0.77 0.68 1.41 1.49 0.72 100%
Bg 1 26 34 10 22 10 8 0.38 0.65 1.13 1.36 0.52 83%
Ch 1 26 34 14 15 19 9 0.54 0.44 0.98 1.12 0.49 95%
Di 1 26 34 14 15 19 9 0.54 0.44 0.98 1.12 0.49 95%
a

Num. models, number of models with CCRtrain and CCRtest ≥ 0.70

b

N(1), number of actives

c

N(0), number of inactives

d

CCRevs, correct classification rate of the consensus models using the external validation set

e

Coverage: percentage of predicted compounds, and coverage = % of the external set compounds predicted by the models

f

A, kNN-Dragon

g

B, kNN-Dragon-NVS where kNN model was generated using all 387 Dragon descriptors with no variable selection and 1 nearest neighbor (NN)

h

C, kNN-Dragon-MFD where the kNN model was generated with top 20 most frequent Dragon descriptors and 1NN

i

D, kNN-Dragon-DWD where the kNN model was generated with top 20 highly weighted Dragon descriptors by DWD and 1 NN.