Transcript Experimental Annotations in ROC Russ Altman, Alain Laederach Based on our experiences with RiboWeb and our participation in a Program Project Grant.

Experimental Annotations in ROC
Russ Altman, Alain Laederach
Based on our experiences with RiboWeb and our
participation in a Program Project Grant
Chalk Talk
Structural Information
• PDB
– Evidence for Structural Motifs
• Base Pairs, Long range interactions etc.
• Experiments
– Many Biochemists getting more or less accurate
structural evidence as well
• DMS Footprinting, Hydroxyl Radical Footprinting
• Tethered BABE probes, FRET, NMR, EPR
– Even computational folks predict structure
• Phylogenetic co-variance analysis
• M-Fold
A possible hierarchy
All_Possible_RNA_Structural_Measurements
Acessibility
ASA PDB
Distance
OH Footprint
PDB Measurement
Cross Linking
FRET
BABE OH
NOE
Phylogenetic BP
Shape
PDB Rg
Stacking
SAXS
2AP
PDB
Why is this useful?
• We can populate instances from PDB
• We can also populate from experiments
– Biochemical
– Computational
• For structure prediction:
– Make PDB from ensemble of biochemical data