Welcome to RNApdbee, a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs.

RNApdbee runs according to the following scenarios:

In both scenarios, the resulting secondary structure encoded in dot-bracket, BPSEQ and CT is immediately released together with a graphical image (if checked).


1)
Upload RNA 3D structure:
 
– from Protein Data Bank
 
– from local file

 
– from PDB example
Data uploaded from: - (no file selected)

2)
Identify base-pairs using:
RNAView
MC-Annotate
3DNA/DSSR Analyse helices

 
and include non-canonical ones:
in text and graphical representation
in graphical representation only
do not include

3)
Resolve & encode secondary structure topology using:
Hybrid Algorithm
Dynamic Programming
Elimination Min-Gain
Elimination Max-Conflicts
First-Come-First-Served

4)
Generate graphical image using: (Note)
PseudoViewer-based procedure
VARNA-based procedure
No image

5)
1)
Upload RNA base-pair list:
 
– from local file (BPSEQ/CT)

 
– from BPSEQ example
 
– from CT example
Data uploaded from: - (no file selected)

2)
Resolve & encode secondary structure topology using:
Hybrid Algorithm
Dynamic Programming
Elimination Min-Gain
Elimination Max-Conflicts
First-Come-First-Served

3)
Generate graphical image using: (Note)
PseudoViewer-based procedure
VARNA-based procedure
No image

4)