Classical RNA loop motifs

[febos]

Dear Dr. Lu,

As I understand correctly, for the moment there is no program (or database) that annotates (or stores) classical RNA loop motifs explicitly.
By the classical RNA loop motifs I mean sarcin/ricin loop, E-loop, tandem sheared G-A, GA/AAG internal loop, UAA/GAN internal loop, kink-turn, etc.

As I know it:
1) only kink-turns are annotated by DSSR.
2) for sarcin/ricin loop, E-loop, and tandem sheared G-A the best way of annotation is to use manually curated annotation from RNAMotifContrast and merge it with the RNA Motif Atlas clusters' identifiers.
3) for GA/AAG internal loop and UAA/GAN internal loop annotation there are no existing ways at all.

If I'm wrong, could you please let me know if I missed anything?
If I'm right, are there any plans to add the mentioned motifs to DSSR functionality in the future?

Thanks in advance!

Best regards,
Eugene Baulin

[xiangjun]

Hi Dr. Baulin,

As I understand correctly, for the moment there is no program (or database) that annotates (or stores) classical RNA loop motifs explicitly.
By the classical RNA loop motifs I mean sarcin/ricin loop, E-loop, tandem sheared G-A, GA/AAG internal loop, UAA/GAN internal loop, kink-turn, etc.

You may be right. Your list of 'classical RNA loop motifs' includes `etc.` and I am not sure/aware of the complete list.

As I know it:
1) only kink-turns are annotated by DSSR.

DSSR isn't intended to be a comprehensive tool for annotating 'classical RNA loop motifs.' DSSR, on the other hand, includes the fundamentals (such as base-pairing/stacking annotations and backbone torsions) that should make any downstream pipeline easier to annotate any well-defined RNA structural motifs.

DSSR can auto-detect kink-turns because K-turns have striking structural features and important functional roles, and I want to have a thorough understanding of the motif. Personally, I've found that only by implementing a topic/concept in detail source code can I truly comprehend it.

The Tamar Schlick made use of this DSSR features in their 2017 NAR paper "Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction." Please take a look at the following two threads (which also demonstrate the value of the 3DNA Forum) initiated by lead author of the paper:

• "Bending angle of internal loops"
• "1MZP"

2) for sarcin/ricin loop, E-loop, and tandem sheared G-A the best way of annotation is to use manually curated annotation from RNAMotifContrast and merge it with the RNA Motif Atlas clusters' identifiers.

RNAMotifContrast and RNA Motif Atlas clusters are certainly well-known resources on the topic. Another source of information that is worth checking is the Janusz Bujnicki lab website.

3) for GA/AAG internal loop and UAA/GAN internal loop annotation there are no existing ways at all.

DSSR has a dedicated section of ALL internal loops. Filtered by sequence constraints and geometric constraints, you might find what you're looking for.

If I'm wrong, could you please let me know if I missed anything?
If I'm right, are there any plans to add the mentioned motifs to DSSR functionality in the future?

In the future, I may add more motif annotations to DSSR Pro.

Best regards,

Xiang-Jun