remembrances of things past
DESCRIPTION
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’ - PowerPoint PPT PresentationTRANSCRIPT
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 Cluster Resultsdinucleotide backbone
ARNADRB006CGPF
URB003ApA - Ca4
DRB003ApU - 9AA
URB008UPA1
URB008UPA2
Cluster 2
Cluster 1
RMSD Cluster Resultssuite backbone
ARNA
DRB006CGPF
URB003ApA - Ca4
DRB003ApU - 9AA
URB008UPA1
URB008UPA2
RMSD Cluster Results backbone plus chi
ARNA
DRB006CGPF URB003
ApA - Ca4
DRB003ApU - 9AAURB008
UPA1
URB008UPA2
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