RNA Structure, Function & Design
Much of RNA biology only comes into focus once structure, folding, and molecular context are taken seriously. I have been developing and teaching these methods since the early days of the ViennaRNA Package. What you find here is the practical side of that work.
RNAfold tutorial: MFE, pair probabilities and ensemble output
How to read RNAfold output in ViennaRNA: minimum free energy structure, pair probabilities, centroid and MEA structures, and when the MFE structure misleads.
28 October 2026Read → TutorialSHAPE and chemical probing tutorial: folding with reactivities in RNAfold
How to use SHAPE and chemical probing reactivities in RNAfold: the input format, the Deigan, Zarringhalam and Washietl methods, and what the data change.
19 October 2026Read → BackgroundAI for RNA structure prediction: what deep learning models learn
What AI models for RNA secondary structure prediction learn from biased data, how to evaluate them on unseen families, and what has changed since 2022.
28 October 2026Read →Guides · RNA structure prediction with ViennaRNA
All tutorials and background reading →Latest writing
All posts →Claude Code, Codex, OpenCode and pi against ten local models on a two-Mac exo cluster
I ran Claude Code, Codex, OpenCode and pi against the ten models that are downloaded on my exo cluster (two Mac minis with 24 GB each), with the same one-line editing...
ViennaRNA 2.8.0: cross-linking data, global probabilities, modified RNA
ViennaRNA 2.8.0 was released on 6 November 2026. Cross-linking experiments can now guide a structure prediction through interval-pair constraints, equilibrium...
RNAplfold tutorial: accessibility in long RNAs
How to compute the accessibility of a region with RNAplfold in the ViennaRNA Package, i.e. the probability that a stretch of nucleotides is unpaired, how to read the...
Computational RNA biology
RNA structure prediction · folding kinetics · functional RNA design · viral RNA biology · RNA–protein recognition · reproducible methods
PublicationsPapers, talks and posters
The complete list since 2002, every paper with abstract, DOI and PDF.
Independent research platformRNA Forecast
Current projects, software, and the ViennaRNA training in preparation for 2027. rnaforecast.com →