Remembrances of Things Past

Comparison of RNA conformers with very small RNA crystal structures Clustered the conformers Compared with dinucleoside phosphates –High resolution –With and without ligands

RMSD Clustering Hierarchical clustering using ‘complete linkages’ Cluster data set included: – 38 model dinucleotides representing the diversity of RNA conformation space (earlier version) – 7 high resolution dinucleoside phosphate crystal structures Clustered families based on backbone RMSD

RMSD clustering P-O5’-C5’-C4-’C3-O3’-P-O5’-C5’C4’-C3’-O3’ No base atoms included in calculations

RMSD Cluster Results ARNA DRB006 CGPF

All A RNA-like conformers

Subtle backbone changes affect base geometry and function

RMSD Cluster Results URB008 UPA2 Cluster 2 Cluster 1

UpA 2 an open conformation

UpA 2 like conformers

RMSD Cluster Results URB003 ApA - Ca++ DRB003 ApU - 9AA URB008 UPA1

UpA1 helix turner

UpA1 like conformers small backbone changes make big structural changes

RMSD Cluster Results dinucleotide backbone ARNA DRB006 CGPF URB003 ApA - Ca4 DRB003 ApU - 9AA URB008 UPA1 URB008 UPA2 Cluster 2 Cluster 1

RMSD Cluster Results suite backbone ARNA DRB006 CGPF URB003 ApA - Ca4 DRB003 ApU - 9AA URB008 UPA1 URB008 UPA2

RMSD Cluster Results backbone plus chi ARNA DRB006 CGPF URB003 ApA - Ca4 DRB003 ApU - 9AA URB008 UPA1 URB008 UPA2

myRNAdb MySQL relational database of ~1000 RNA containing structures in NDB/PDB Uses core schema based on mmCIF/PDB Exchange Dictionary Includes base-pair and base-pair step geometries and RNA SCOR annotation Warehouse style tables for mining nucleotide, dinucleotide and trinucleotide features. Python tools for loading, access and analysis