The Circular Diagram Server is under construction as of November 4, 2024.
The Circular Diagram Server creates 2D diagrams showing interactions within RNA and DNA structures. The server reduces intricate details from 3D RNA structures to a comprehensible one-page 2D format, maintaining essential information while simplifying visualization. Users can customize the diagram in several ways. Clicking Submit will generate a diagram in PDF format. For further guidance, click on the "Help" button above.
| Show | Dim | Hide | Interaction |
|---|---|---|---|
| nested Watson-Crick basepairs | |||
| non-nested Watson-Crick basepairs | |||
| nested non-Watson-Crick basepairs | |||
| non-nested non-Watson-Crick basepairs | |||
| stacking interactions | |||
| base-phosphate interactions | |||
| base-ribose interactions | |||
| near interactions |
Example 1
Complete Escherichia coli ribosome showing the 5S chain, large subunit, small subunit,
and two tRNAs bound to the LSU and SSU and interacting with mRNA.
Example 2
Human large ribosomal subunit and 5.8S chain. These chains have more than 5000 nucleotides,
but large segments of chain L5 do not have 3D coordinates in the solved structure, and so are represented with base and sequence position only.
Stacking and near interactions are not shown, and base-backbone interactions are dimmed.
Example 3
This eukaryotic ribozyme from Tetrahymena features a pseudoknot and kissing hairpins between nucleotides G44 and C170.
It also includes a cis Watson-Crick/Watson-Crick (cWW) interaction between G100 and C274. G100 is located in the linker
region between helices, while C274 is situated on one strand of an internal loop.
Example 4
This presents the 8OM4 molecule, which is a mitochondrial small subunit ribosomal RNA (SSU rRNA)
from Saccharomyces cerevisiae, commonly known as baker's yeast. The diagram employs grayscale
coloring and highlights only the nested cWW interactions while reducing the prominence of long-range cWW interactions.