Welcome to RNApdbee, a webserver to annotate secondary structures of knotted and unknotted RNAs.

RNApdbee runs according to the following scenarios:

In the first and the second scenario, the resulting secondary structure encoded in dot-bracket, BPSEQ and CT is immediately released together with visualization (if checked).


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

 
– from PDB example
1 2 3 4 5 6
 
– from PDBx/mmCIF example
1 2 3 4 5 6
Data uploaded from: - (no file selected)

2)
Select:
first model only
all models

3)
Identify base pairs using:
3DNA/DSSR Analyse helices
RNAView
MC-Annotate
FR3D

 
Include non-canonical ones:
in visualization only
in text and visualization
do not include

 
Remove isolated, canonical base pairs:


4)
Resolve & encode secondary structure topology using:
Hybrid Algorithm ?
Dynamic Programming ?
Elimination Min-Gain ?
Elimination Max-Conflicts ?
First-Come-First-Served ?

5)
Identify structural elements treating pseudoknots as:
Paired residues
Unpaired residues

6)
Visualize secondary structure using:
VARNA-based procedure
PseudoViewer-based procedure
R-chie
No image

7)
1)
Upload RNA base pair list:
 
– from local file (BPSEQ/CT)

 
– from BPSEQ example
1 gateio app 3
 
– from CT example
1 2 gate io login
Data uploaded from: - (no file selected)

2)
Remove isolated, canonical base pairs:



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

4)
Identify structural elements treating pseudoknots as:
Paired residues
Unpaired residues

5)
Visualize secondary structure using:
VARNA-based procedure
PseudoViewer-based procedure
R-chie
No image

6)
1)
Upload dot-bracket:
 
– from local file

 
– from example
1 2 3
Data uploaded from: - (no file selected)

2)
Identify structural elements treating pseudoknots as:
Paired residues
Unpaired residues

3)
Visualize secondary structure using:
VARNA-based procedure
PseudoViewer-based procedure
R-chie

4)
1)
Upload RNA 3D structure:
 
– from Protein Data Bank
 
– from local file

 
– from PDB example
1 2 3 4 5
 
– from PDBx/mmCIF example
1 gate.io 3 4 gate io app
Data uploaded from: - (no file selected)

2)
Select:
first model only
all models

3)
During base pair identification:
include non-canonical base pairs
remove isolated, canonical base pairs

4)
Visualize secondary structure using:
VARNA-based procedure
PseudoViewer-based procedure
R-chie
No image

5)