geometric classification of rna conformations potts model classification (data clustering using...
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![Page 1: Geometric classification of RNA conformations Potts model classification (Data clustering using model granular magnets M. Blatt, S. Weisman. E. Domany](https://reader035.vdocuments.site/reader035/viewer/2022062421/56649d785503460f94a5a628/html5/thumbnails/1.jpg)
Geometric classification of RNA conformations
Potts model classification
(Data clustering using model granular magnets M. Blatt, S. Weisman. E. Domany
Neural Computation 1997)
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Validation
• RNA Backbone conformations: Data file RR0033. Binning
• Base pairs interactions: Data file RR0082
LW ROC annotation.
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Backbone conformations RR0033
00.1
0.20.3
0.40.5
0.60.7
0.80.9
1
00.1
0.20.3
0.40.5
0.6
0.70.8
0.9
0.4
0.5
0.6
0.7
0.8
0.9
1
cluster 1cluster 2
cluster 3
cluster 4
cluster 5
cluster 6cluster 7
cluster 8
cluster 9
cluster 10cluster 11
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Backbone binning RR0033
00.1
0.20.3
0.40.5
0.60.7
0.80.9
1
00.1
0.20.3
0.40.5
0.6
0.70.8
0.9
0.4
0.5
0.6
0.7
0.8
0.9
1
a
oi
r
u
s
cd
l
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Coordinates
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cWW(GU)
cWW
cWW(UG)
cWW(CU)
tHS(AG O2’)
tSH
tHS(AG O4’)
csS
tHS(AC)
tHW(AU)
CSs+CsS
t-loop
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cHW+cHS)
tWW
thH
tWS
cHS
tsS
tSs(AG)+tsS(CA)
tSW(GA)
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Base stacking
• Four relatives geometries of the base stacking.
• Trying to minimize the number of coordinates.
• Data base RR0033, RR0153,RR0154.
• Comparing with less accurate data of e-coli RR0228, RR0229.
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Allstacking up-down T=.145
pyr-pyrpyr-pur
pur-pyr
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Content classes
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0S-1 (10,1)
0S-2,3 (1,10)
0S-4
Up-down T=0.112
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Stacking group up-downAllstacking 0 E-coli 0
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Stacking up-down
All stacking t=.12 E-coli t=0.112
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down-down stacking
All stacking t=.0251E-coli t =.0241
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Down-up stacking
All stacking t=0.055 E-coli t = .081