Difference between revisions of "DOCK Benchmarking"

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Line 29: Line 29:
 
| <center>'''Experiment'''</center>
 
| <center>'''Experiment'''</center>
 
| <center>'''Results'''</center>
 
| <center>'''Results'''</center>
−
| <center>'''Timing'''</center>
+
| <center>'''Timing (s)'''</center>
 
| <center>'''DOCK Version'''</center>
 
| <center>'''DOCK Version'''</center>
 
| <center>'''Notes'''</center>
 
| <center>'''Notes'''</center>
Line 37: Line 37:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, Grid</center>
 
| <center>PR, Grid</center>
−
| <center>-</center>
+
| <center>Success 762 0.73058485139 Scoring 183 0.175455417066 Sampling 98 0.0939597315436</center>
−
| <center>-</center>
+
| <center>263</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 46: Line 46:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, Ph4</center>
 
| <center>PR, Ph4</center>
−
| <center>-</center>
+
| <center>Success 986 0.945349952061 Scoring 19 0.0182166826462 Sampling 38 0.0364333652924
−
| <center>-</center>
+
</center>
 +
| <center>1029</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 55: Line 56:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_Ph4</center>
 
| <center>PR, desc_Ph4</center>
−
| <center>-</center>
+
| <center>Success 986 0.945349952061 Scoring 19 0.0182166826462 Sampling 38 0.0364333652924</center>
−
| <center>-</center>
+
| <center>1077</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 64: Line 65:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_VO</center>
 
| <center>PR, desc_VO</center>
−
| <center>-</center>
+
| <center>Success 841 0.806327900288 Scoring 42 0.0402684563758 Sampling 160 0.153403643337</center>
−
| <center>-</center>
+
| <center>745</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 73: Line 74:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid+1Ph4</center>
 
| <center>PR, desc_1Grid+1Ph4</center>
−
| <center>-</center>
+
| <center>Success 874 0.837967401726 Scoring 116 0.111217641419 Sampling 53 0.0508149568552</center>
−
| <center>-</center>
+
| <center>1248</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 82: Line 83:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid+10Ph4</center>
 
| <center>PR, desc_1Grid+10Ph4</center>
−
| <center>-</center>
+
| <center>Success 1023 0.980824544583 Scoring 13 0.0124640460211 Sampling 7 0.00671140939597</center>
−
| <center>-</center>
+
| <center>1168</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 91: Line 92:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid-1VO</center>
 
| <center>PR, desc_1Grid-1VO</center>
−
| <center>-</center>
+
| <center>Success 780 0.747842761266 Scoring 165 0.158197507191 Sampling 98 0.0939597315436</center>
−
| <center>-</center>
+
| <center>1037</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 100: Line 101:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid-20VO</center>
 
| <center>PR, desc_1Grid-20VO</center>
−
| <center>-</center>
+
| <center>Success 933 0.894534995206 Scoring 71 0.0680728667306 Sampling 39 0.0373921380633</center>
−
| <center>-</center>
+
| <center>1027</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 109: Line 110:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid-1TAN</center>
 
| <center>PR, desc_1Grid-1TAN</center>
−
| <center>-</center>
+
| <center>Success 742 0.711409395973 Scoring 170 0.162991371045 Sampling 131 0.125599232982</center>
−
| <center>-</center>
+
| <center>5932</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 118: Line 119:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid-20TAN</center>
 
| <center>PR, desc_1Grid-20TAN</center>
−
| <center>-</center>
+
| <center>Success 752 0.720997123682 Scoring 169 0.162032598274 Sampling 122 0.116970278044</center>
−
| <center>-</center>
+
| <center>5992</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 127: Line 128:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid+1HUN</center>
 
| <center>PR, desc_1Grid+1HUN</center>
−
| <center>-</center>
+
| <center>Success 895 0.858101629914 Scoring 106 0.10162991371 Sampling 42 0.0402684563758</center>
−
| <center>-</center>
+
| <center>2949</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 136: Line 137:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid+10HUN</center>
 
| <center>PR, desc_1Grid+10HUN</center>
−
| <center>-</center>
+
| <center>Success 1029 0.986577181208 Scoring 4 0.00383509108341 Sampling 10 0.00958772770853</center>
−
| <center>-</center>
+
| <center>2204</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 145: Line 146:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid+1Ph4-1VO</center>
 
| <center>PR, desc_1Grid+1Ph4-1VO</center>
−
| <center>-</center>
+
| <center>Success 879 0.84276126558 Scoring 127 0.121764141898 Sampling 37 0.0354745925216</center>
−
| <center>-</center>
+
| <center>1951</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 154: Line 155:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid+5Ph4-10VO</center>
 
| <center>PR, desc_1Grid+5Ph4-10VO</center>
−
| <center>-</center>
+
| <center>Success 1009 0.967401725791 Scoring 25 0.0239693192713 Sampling 9 0.00862895493768</center>
−
| <center>-</center>
+
| <center>1876</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 163: Line 164:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid+1Ph4-1TAN</center>
 
| <center>PR, desc_1Grid+1Ph4-1TAN</center>
−
| <center>-</center>
+
| <center>Success 853 0.817833173538 Scoring 113 0.108341323106 Sampling 77 0.0738255033557</center>
−
| <center>-</center>
+
| <center>6539</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 172: Line 173:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid+5Ph4-10TAN</center>
 
| <center>PR, desc_1Grid+5Ph4-10TAN</center>
−
| <center>-</center>
+
| <center>Success 962 0.922339405561 Scoring 41 0.039309683605 Sampling 40 0.0383509108341</center>
−
| <center>-</center>
+
| <center>6366</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 181: Line 182:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid+1Ph4+1HUN</center>
 
| <center>PR, desc_1Grid+1Ph4+1HUN</center>
−
| <center>-</center>
+
| <center>Success 946 0.906999041227 Scoring 63 0.0604026845638 Sampling 34 0.032598274209</center>
−
| <center>-</center>
+
| <center>3612</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 190: Line 191:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid+5Ph4+5HUN</center>
 
| <center>PR, desc_1Grid+5Ph4+5HUN</center>
−
| <center>-</center>
+
| <center>Success 1021 0.978906999041 Scoring 3 0.00287631831256 Sampling 19 0.0182166826462</center>
−
| <center>-</center>
+
| <center>3059</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 199: Line 200:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid-1VO-1TAN</center>
 
| <center>PR, desc_1Grid-1VO-1TAN</center>
−
| <center>-</center>
+
| <center>Success 772 0.740172579099 Scoring 160 0.153403643337 Sampling 111 0.106423777565</center>
−
| <center>-</center>
+
| <center>6489</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 208: Line 209:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid-10VO-10TAN</center>
 
| <center>PR, desc_1Grid-10VO-10TAN</center>
−
| <center>-</center>
+
| <center>Success 856 0.82070949185 Scoring 106 0.10162991371 Sampling 81 0.0776605944391</center>
−
| <center>-</center>
+
| <center>6456</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 217: Line 218:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid-1VO+1HUN</center>
 
| <center>PR, desc_1Grid-1VO+1HUN</center>
−
| <center>-</center>
+
| <center>Success 900 0.862895493768 Scoring 98 0.0939597315436 Sampling 45 0.0431447746884</center>
−
| <center>-</center>
+
| <center>3555</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
Line 226: Line 227:
 
| <center>2015.11.01, Yuchen</center>
 
| <center>2015.11.01, Yuchen</center>
 
| <center>PR, desc_1Grid-10VO+5HUN</center>
 
| <center>PR, desc_1Grid-10VO+5HUN</center>
−
| <center>-</center>
+
| <center>Success 1017 0.975071907958 Scoring 7 0.00671140939597 Sampling 19 0.0182166826462</center>
−
| <center>-</center>
+
| <center>2946</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
 
|-
 
|-
 +
  
 
| <center>2015.11.04, Yuchen</center>
 
| <center>2015.11.04, Yuchen</center>
 
| <center>Rescoring, Hawkins_GBSA</center>
 
| <center>Rescoring, Hawkins_GBSA</center>
 +
| <center>Success 749 0.718120805369 Scoring 196 0.187919463087 Sampling 98 0.0939597315436</center>
 
| <center>-</center>
 
| <center>-</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 +
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid-40VO</center>
 +
| <center>Success 991 0.950143815916 Scoring 29 0.0278044103547 Sampling 23 0.0220517737296</center>
 +
| <center>1003</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
 +
|-
 +
 +
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_-40VO</center>
 +
| <center>Success 1041 0.998082454458 Scoring 0 0.0 Sampling 2 0.00191754554171</center>
 +
| <center>702</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>DOCK6.8.2015.10.30</center>
 
| <center>-</center>
 
| <center>-</center>
 
|-
 
|-

Revision as of 01:52, 12 November 2015

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 762 0.73058485139 Scoring 183 0.175455417066 Sampling 98 0.0939597315436
263
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, Ph4
Success 986 0.945349952061 Scoring 19 0.0182166826462 Sampling 38 0.0364333652924
1029
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_Ph4
Success 986 0.945349952061 Scoring 19 0.0182166826462 Sampling 38 0.0364333652924
1077
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_VO
Success 841 0.806327900288 Scoring 42 0.0402684563758 Sampling 160 0.153403643337
745
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+1Ph4
Success 874 0.837967401726 Scoring 116 0.111217641419 Sampling 53 0.0508149568552
1248
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+10Ph4
Success 1023 0.980824544583 Scoring 13 0.0124640460211 Sampling 7 0.00671140939597
1168
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-1VO
Success 780 0.747842761266 Scoring 165 0.158197507191 Sampling 98 0.0939597315436
1037
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-20VO
Success 933 0.894534995206 Scoring 71 0.0680728667306 Sampling 39 0.0373921380633
1027
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-1TAN
Success 742 0.711409395973 Scoring 170 0.162991371045 Sampling 131 0.125599232982
5932
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-20TAN
Success 752 0.720997123682 Scoring 169 0.162032598274 Sampling 122 0.116970278044
5992
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+1HUN
Success 895 0.858101629914 Scoring 106 0.10162991371 Sampling 42 0.0402684563758
2949
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+10HUN
Success 1029 0.986577181208 Scoring 4 0.00383509108341 Sampling 10 0.00958772770853
2204
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+1Ph4-1VO
Success 879 0.84276126558 Scoring 127 0.121764141898 Sampling 37 0.0354745925216
1951
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+5Ph4-10VO
Success 1009 0.967401725791 Scoring 25 0.0239693192713 Sampling 9 0.00862895493768
1876
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+1Ph4-1TAN
Success 853 0.817833173538 Scoring 113 0.108341323106 Sampling 77 0.0738255033557
6539
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+5Ph4-10TAN
Success 962 0.922339405561 Scoring 41 0.039309683605 Sampling 40 0.0383509108341
6366
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+1Ph4+1HUN
Success 946 0.906999041227 Scoring 63 0.0604026845638 Sampling 34 0.032598274209
3612
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid+5Ph4+5HUN
Success 1021 0.978906999041 Scoring 3 0.00287631831256 Sampling 19 0.0182166826462
3059
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-1VO-1TAN
Success 772 0.740172579099 Scoring 160 0.153403643337 Sampling 111 0.106423777565
6489
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-10VO-10TAN
Success 856 0.82070949185 Scoring 106 0.10162991371 Sampling 81 0.0776605944391
6456
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-1VO+1HUN
Success 900 0.862895493768 Scoring 98 0.0939597315436 Sampling 45 0.0431447746884
3555
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-10VO+5HUN
Success 1017 0.975071907958 Scoring 7 0.00671140939597 Sampling 19 0.0182166826462
2946
DOCK6.8.2015.10.30
-
2015.11.04, Yuchen
Rescoring, Hawkins_GBSA
Success 749 0.718120805369 Scoring 196 0.187919463087 Sampling 98 0.0939597315436
-
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_1Grid-40VO
Success 991 0.950143815916 Scoring 29 0.0278044103547 Sampling 23 0.0220517737296
1003
DOCK6.8.2015.10.30
-
2015.11.01, Yuchen
PR, desc_-40VO
Success 1041 0.998082454458 Scoring 0 0.0 Sampling 2 0.00191754554171
702
DOCK6.8.2015.10.30
-
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