Difference between revisions of "DOCK Benchmarking"

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(Created page with "{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%" |- style="background:cornflowerblue" | <center>'''Date, Autho...")
 
 
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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"
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{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"
 
{| align="center" border="1" cellpadding="8" cellspacing="0" style="background:white; text-align:left; width:95%"
 
|- style="background:cornflowerblue"
 
|- style="background:cornflowerblue"
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| <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>
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−
| <center>2015.08.24 Mon</center>
+
| <center>2015.11.01, Yuchen</center>
−
||  
+
| <center>PR, Grid</center>
−
*''Organizational Meeting
+
| <center>Success 73.1% Scoring 17.5% Sampling 9.4%</center>
−
|| <center>-</center>
+
| <center>263</center>
−
|| <center>-</center>
+
| <center>DOCK6.8.2015.10.30</center>
−
|| <center>-</center>
+
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, Ph4</center>
 +
| <center>Success 94.5% Scoring 1.8% Sampling 3.6%</center>
 +
| <center>1029</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_Ph4</center>
 +
| <center>Success 94.5% Scoring 1.8% Sampling 3.6%</center>
 +
| <center>1077</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_VO</center>
 +
| <center>Success 80.6% Scoring 4.1% Sampling 160 15.3%</center>
 +
| <center>745</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.06, Yuchen</center>
 +
| <center>PR, desc_-40VO</center>
 +
| <center>Success 99.8% Scoring 0 Sampling 0.2%</center>
 +
| <center>702</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid+1Ph4</center>
 +
| <center>Success 83.8% Scoring 11.1% Sampling 5.1%</center>
 +
| <center>1248</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid+10Ph4</center>
 +
| <center>Success 98.1% Scoring 1.2% Sampling 0.7%</center>
 +
| <center>1168</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid-1VO</center>
 +
| <center>Success 74.8% Scoring 15.8% Sampling 9.4%</center>
 +
| <center>1037</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid-20VO</center>
 +
| <center>Success 89.5% Scoring 6.8% Sampling 3.7%</center>
 +
| <center>1027</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.06, Yuchen</center>
 +
| <center>PR, desc_1Grid-40VO</center>
 +
| <center>Success 95% Scoring 2.8% Sampling 2.2%</center>
 +
| <center>1003</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid-1TAN</center>
 +
| <center>Success 71.1% Scoring 16.3% Sampling 12.6%</center>
 +
| <center>5932</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid-20TAN</center>
 +
| <center>Success 72.1% Scoring 16.2% Sampling 11.7%</center>
 +
| <center>5992</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid+1HUN</center>
 +
| <center>Success 85.8% Scoring 10.2% Sampling 4%</center>
 +
| <center>2949</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid+10HUN</center>
 +
| <center>Success 98.6% Scoring 4 0.4% Sampling 1%</center>
 +
| <center>2204</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid+1Ph4-1VO</center>
 +
| <center>Success 84.3% Scoring 12.2% Sampling 3.5%</center>
 +
| <center>1951</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid+5Ph4-10VO</center>
 +
| <center>Success 96.7% Scoring 2.4% Sampling 0.9%</center>
 +
| <center>1876</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid+1Ph4-1TAN</center>
 +
| <center>Success 81.8% Scoring 10.8% Sampling 7.4%</center>
 +
| <center>6539</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid+5Ph4-10TAN</center>
 +
| <center>Success 92.2% Scoring 3.9% Sampling 3.8%</center>
 +
| <center>6366</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid+1Ph4+1HUN</center>
 +
| <center>Success 90.7% Scoring 6% Sampling 3.3%</center>
 +
| <center>3612</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid+5Ph4+5HUN</center>
 +
| <center>Success 97.9% Scoring 0.3% Sampling 1.8%</center>
 +
| <center>3059</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid-1VO-1TAN</center>
 +
| <center>Success 74% Scoring 15.3% Sampling 10.6%</center>
 +
| <center>6489</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid-10VO-10TAN</center>
 +
| <center>Success 82.1% Scoring 10.2% Sampling 7.8%</center>
 +
| <center>6456</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid-1VO+1HUN</center>
 +
| <center>Success 86.3% Scoring 9.4% Sampling 4.3%</center>
 +
| <center>3555</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.01, Yuchen</center>
 +
| <center>PR, desc_1Grid-10VO+5HUN</center>
 +
| <center>Success 97.5% Scoring 0.7% Sampling 1.8%</center>
 +
| <center>2946</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 +
|-
 +
 
 +
 
 +
| <center>2015.11.04, Yuchen</center>
 +
| <center>Rescoring, Hawkins_GBSA</center>
 +
| <center>Success 71.8% Scoring 18.8% Sampling 9.4%</center>
 +
| <center>-</center>
 +
| <center>DOCK6.8.2015.10.30</center>
 +
| <center>-</center>
 
|-
 
|-

Latest revision as of 02:15, 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 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
-
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