how can I predict the interface site of RNA with protein

Question

[bangbang3332]

hi, I have a protein(PDB file) and an RNA sequence(5000bp, fasta file). I want to find the binding site in RNA sequence with the protein, which web server should I choose?

Thank you in advance!

[natasha.sernova]

1) See this article from 2011, it compares many tools.

Predicting RNA-Protein Interactions Using OnlySequence Information

Usha K Muppirala1,2*, Vasant G Honavar1,3and Drena Dobbs1,2

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3322362/pdf/1471-2105-12-489.pdf

and update from 2017:

https://link.springer.com/book/10.1007/978-1-4939-6716-2

2)The second link is more recent, it is a review from 2015.

Review. Computational Prediction of RNA-Binding Proteinsand Binding Sites

Jingna Si *, Jing Cui, Jin Cheng and Rongling Wu

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4661811/pdf/ijms-16-25952.pdf

3) See also this post:

Prediction of RNA binding regions in protein

and https://omictools.com/protein-rna-interactions-category inside

[bangbang3332]

thanks for your help , that is really helpful!

but i also meet with some problems.

i have notice the review from 2015 this morning, Computational Prediction of RNA-Binding Proteinsand Binding Sites . and i tried all the methods mentioned in the paper. but it turned out that most of the tools can not been used anymore. they had been shut down. and the left tools can not meet my quest. i wanna seek the prediction site between specific protein and mRNA. and i want to use the tertiary structure of the protein. i also tried the methods mentioned on OMICTOOLS. but none of them can met my request.

[bangbang3332]

[natasha.sernova]

I see. You need a different approach, like this one.

https://github.com/xypan1232/iDeepE

or this one:

https://www.advancedsciencenews.com/recent-methodology-progress-of-deep-learning-for-rna-protein-interaction-prediction/

Good luck!

[bangbang3332]

hahaha，i also tried that one yesterday! but that approach needs the protein-rna interaction database of the protein that you want to study to train the model. Finally, i used the catRAPID. it finally solved my problems...Thanks a lot!!!!

Answer 1

[bangbang3332]

hahaha，i also tried that one yesterday! but that approach needs the protein-rna interaction database of the protein that you want to study to train the model. Finally, i used the catRAPID. it finally solved my problems...Thanks a lot!!!!