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. Author manuscript; available in PMC: 2015 May 14.
Published in final edited form as: Methods. 2014 Sep 8;71:77–84. doi: 10.1016/j.ymeth.2014.08.017

Table 2.

Enrichment rate (ER) values for the top 1%, 5% and 10% compounds (ER1%, ER5% and ER10%) on 20 DUD targets using different receptor models with or without Tanimoto filters (“−” refers to the cases which failed to achieve enrichment over random screening).

Targets Original DUD dataset without filter
TC2 dataset with TanimotoCombo filter
Crystal (bound)
Crystal (relaxed)
I-TASSER model
Crystal (bound)
I-TASSER model
ER1% ER5% ER10% ER1% ER5% ER10% ER1% ER5% ER10% ER1% ER5% ER10% ER1% ER5% ER10%
ace 25.00 39.58 39.58 20.41 28.57 36.73 18.37 30.61 34.69 45.83 66.67 66.67 33.33 50.00 58.33
ada 15.38 25.64 38.46 12.82 28.21 38.46 5.13 17.95 41.03 15.38 25.64 38.46 5.13 17.95 41.03
ampc 14.29 28.57 33.33 19.05 28.57 38.10 – – – 15.00 30.00 35.00 – – –
cdk2 19.72 30.99 33.80 12.50 18.06 19.44 14.08 25.35 28.17 19.72 30.99 33.80 14.08 25.35 28.17
comt 11.11 11.11 11.11 – 12.50 12.50 27.27 27.27 27.27 – – – 100.00 100.00 100.00
egfr 19.36 30.85 35.74 23.26 33.40 38.48 21.43 25.76 28.57 17.19 28.73 33.94 20.00 24.09 27.05
fgfr1 11.40 20.18 22.81 21.93 35.09 40.35 16.07 28.57 32.14 12.87 21.78 24.75 17.17 27.27 31.31
hivrt 11.63 20.93 30.23 4.65 13.95 18.60 11.63 18.60 20.93 12.82 20.51 28.21 12.82 15.38 17.95
inha 16.87 30.12 32.53 16.67 25.00 28.57 18.60 31.40 34.88 15.38 28.21 32.05 18.52 29.63 33.33
mr 13.33 33.33 46.67 6.67 6.67 13.33 6.67 6.67 6.67 15.38 38.46 46.15 – – –
na 26.53 55.10 67.35 2.04 10.20 12.24 14.29 26.53 40.82 25.00 54.17 66.67 14.58 27.08 39.58
p38 11.92 18.98 22.30 12.99 21.11 27.84 8.89 16.89 22.00 15.79 18.95 22.63 11.83 16.67 20.97
parp 17.14 20.00 31.43 14.71 17.65 20.59 2.86 2.86 2.86 17.14 20.00 31.43 2.86 2.86 2.86
pde5 18.18 31.82 34.09 14.77 26.14 28.41 15.48 26.19 29.76 9.09 11.36 13.64 6.67 8.89 11.11
pnp 14.00 16.00 26.00 – – 4.00 16.00 22.00 26.00 14.00 16.00 26.00 16.00 22.00 26.00
rxr-a 20.00 50.00 50.00 30.00 45.00 45.00 – – – 20.00 50.00 50.00 – – –
src 21.66 28.03 31.21 18.54 27.81 28.48 15.23 27.81 31.13 – – 8.33 7.32 14.63 17.07
thrombin 16.90 46.48 57.75 10.14 26.09 31.88 15.28 44.44 54.17 9.52 23.81 38.10 10.00 25.00 25.00
trypsin 13.64 31.82 38.64 7.14 19.05 33.33 4.26 12.77 21.28 7.14 28.57 28.57 – – –
vegfr2 14.12 15.29 15.29 21.18 34.12 38.82 21.59 25.00 30.68 4.65 6.98 6.98 12.50 12.50 22.50
Average 15.68 26.65 32.37 14.97 24.06 27.76 14.06 23.15 28.50 16.22 28.94 33.23 18.93 26.21 31.39