1 / 18

Geometric classification of RNA conformations

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

jed
Download Presentation

Geometric classification of RNA conformations

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Geometric classification of RNA conformations Potts model classification (Data clustering using model granular magnets M. Blatt, S. Weisman. E. Domany Neural Computation 1997)

  2. Validation • RNA Backbone conformations: Data file RR0033. Binning • Base pairs interactions: Data file RR0082 LW ROC annotation.

  3. Backbone conformations RR0033

  4. Backbone binning RR0033

  5. Coordinates

  6. Up-Down CSs+CsS csS tHW(AU) t-loop tHS(AC) cWW tSH cWW(GU) cWW(UG) tHS(AG O2’) tHS(AG O4’) cWW(CU)

  7. Up-Up cHW+cHS) tWS tSs(AG)+tsS(CA) thH tWW tsS tSW(GA) cHS

  8. 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.

  9. Susceptibility stacking up-down

  10. Allstacking up-down T=.145 pyr-pur pyr-pyr pur-pyr

  11. Content classes

  12. Up-down T=0.112 0S-1 (10,1) 0S-4 0S-2,3 (1,10)

  13. Stacking group up-down Allstacking 0 E-coli 0

  14. Stacking up-down E-coli t=0.112 All stacking t=.12

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

  16. Down-up stacking All stacking t=0.055 E-coli t = .081

More Related