DOCK VS Benchmarking

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ABBREVIATIONS:

PR = Pose Reproduction

VS = Virtual Screening

desc = Descriptor Score

Grid = Grid Score

MG = Multi Grid Score

Ph4 = Pharmacophore Score

HUN = Hungarian RMSD Score

TAN = Tanimoto Score

VO = Volume Overlap Score

Example for combination of scoring functions: desc_1Grid+5Ph4-10VO means descriptor score using combination "Descriptor Score = 1 * Grid Score + 5 * Pharmacophore Socre - 10 * Volume Overlap Score"



Date, Author
Experiment
Results
Timing (s)
DOCK Version
Notes
2015.11.01, Yuchen
PR, Grid
Success 73.1% Scoring 17.5% Sampling 9.4%
263
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, Ph4
Success 94.5% Scoring 1.8% Sampling 3.6%
1029
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_Ph4
Success 94.5% Scoring 1.8% Sampling 3.6%
1077
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_VO
Success 80.6% Scoring 4.1% Sampling 160 15.3%
745
DOCK6.8.2015.10.30
-
2015.11.06, Yuchen
PR, desc_-40VO
Success 99.8% Scoring 0 Sampling 0.2%
702
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+1Ph4
Success 83.8% Scoring 11.1% Sampling 5.1%
1248
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+10Ph4
Success 98.1% Scoring 1.2% Sampling 0.7%
1168
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-1VO
Success 74.8% Scoring 15.8% Sampling 9.4%
1037
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-20VO
Success 89.5% Scoring 6.8% Sampling 3.7%
1027
DOCK6.8.2015.10.30
-
2015.11.06, Yuchen
PR, desc_1Grid-40VO
Success 95% Scoring 2.8% Sampling 2.2%
1003
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-1TAN
Success 71.1% Scoring 16.3% Sampling 12.6%
5932
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-20TAN
Success 72.1% Scoring 16.2% Sampling 11.7%
5992
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+1HUN
Success 85.8% Scoring 10.2% Sampling 4%
2949
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+10HUN
Success 98.6% Scoring 4 0.4% Sampling 1%
2204
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+1Ph4-1VO
Success 84.3% Scoring 12.2% Sampling 3.5%
1951
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+5Ph4-10VO
Success 96.7% Scoring 2.4% Sampling 0.9%
1876
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+1Ph4-1TAN
Success 81.8% Scoring 10.8% Sampling 7.4%
6539
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+5Ph4-10TAN
Success 92.2% Scoring 3.9% Sampling 3.8%
6366
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+1Ph4+1HUN
Success 90.7% Scoring 6% Sampling 3.3%
3612
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+5Ph4+5HUN
Success 97.9% Scoring 0.3% Sampling 1.8%
3059
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-1VO-1TAN
Success 74% Scoring 15.3% Sampling 10.6%
6489
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-10VO-10TAN
Success 82.1% Scoring 10.2% Sampling 7.8%
6456
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-1VO+1HUN
Success 86.3% Scoring 9.4% Sampling 4.3%
3555
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-10VO+5HUN
Success 97.5% Scoring 0.7% Sampling 1.8%
2946
DOCK6.8.2015.10.30
-
2015.11.04, Yuchen
Rescoring, Hawkins_GBSA
Success 71.8% Scoring 18.8% Sampling 9.4%
-
DOCK6.8.2015.10.30
-
2020.05.04, Scott
Flexible Docking
Success 72.96% Scoring 19.08% Sampling 7.96%
132.72
DOCK6.9.release
Used the Long-40 core
2020.08.16, Scott
Flexible Docking
Success 74.11% Scoring 17.55% Sampling 8.34%
100.62
DOCK6.9.release
Used the Long-40 core, Simplex Minimized