Geometric classification of RNA conformations

Potts model classification

(Data clustering using model granular magnets M. Blatt, S. Weisman. E. Domany

Neural Computation 1997)

Validation

• RNA Backbone conformations: Data file RR0033. Binning

• Base pairs interactions: Data file RR0082

LW ROC annotation.

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

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

Coordinates

cWW(GU)

cWW

cWW(UG)

cWW(CU)

tHS(AG O2’)

tSH

tHS(AG O4’)

csS

tHS(AC)

tHW(AU)

CSs+CsS

t-loop

cHW+cHS)

tWW

thH

tWS

cHS

tsS

tSs(AG)+tsS(CA)

tSW(GA)

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.

Allstacking up-down T=.145

pyr-pyrpyr-pur

pur-pyr

Content classes

0S-1 (10,1)

0S-2,3 (1,10)

0S-4

Up-down T=0.112

Stacking group up-downAllstacking 0 E-coli 0

Stacking up-down

All stacking t=.12 E-coli t=0.112

down-down stacking

All stacking t=.0251E-coli t =.0241

Down-up stacking

All stacking t=0.055 E-coli t = .081