Predicting ligand bind to RNA

Question

[CARMEPLAS]

Which would be the best software to predict the binding of specific ligands to a secondary RNA structure?

Answer 1

[Kevin Blighe]

I have not worked in this area; however, your general question will receive my general answer: The Matthews group appears to have worked in RNA secondary structure analysis for many years. You may try to follow their work and reach out to them:

• RNAstructure: web servers for RNA secondary structure prediction and analysis
• RNA Secondary Structure Analysis Using RNAstructure

Also see this previous post, which has no up-votes:

• Secondary Structure Prediction software RNA/DNA

Another related post, on Biology Stack Exchange:

• Use cases of RNA secondary structure prediction

Good luck

Kevin