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RNA 2nd Structure Prediction

✅ : Recommended

I. RNA Secondary Structure Prediction

1. Basics

  • Energy Model - RNAstructure/Mfold and RNAfold
  • ✅ How do RNA folding algorithms work? (Sean R Eddy) 2004 Nature Biotech
  • What is dynamic programming? (Sean R Eddy) 2004 Nature Biotech
  • SCFG Model (Rfam/Infernal)
  • ✅ What is a hidden Markov model? (Sean R Eddy) 2004 Nature Biotech
  • You can read the SCFG section in the book above (《Biological Sequence Analysis》).

2. Recent Research Articles and Reviews

  • ✅ 2025 Nature Communications - RiNALMo: general-purpose RNA language models can generalize well on structure prediction tasks
  • 2025 Genome Biology HydraRNA: a hybrid architecture based full-length RNA language model
  • 2025 Nature Communications - Deep generalizable prediction of RNA secondary structure via base pair motif energy
  • [review] 2023 BIB - Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery
  • [review] 2022 PNAS - Thoughts on how to think (and talk) about RNA structure
  • 2022 Nucleic Acids Research -UFold_fast and accurate RNA secondary structure prediction with deep learning
  • 2020 ICLR - RNA Secondary Structure Prediction By Learning Unrolled Algorithms (Chinese comments)
  • (Transfer learning) 2019 Nature Commn. - SPOT-RNA: RNA secondary structure prediction using an ensemble of two-dimensional deep neural networks and transfer learning

II. Structure Probing Experiments

1. Structure probing methods

关于RNA 二级结构高通量测序方法

2. Structure probing data analysis

  • 2022 Nature Methods - RNA secondary structure packages evaluated and improved by high-throughput experiments
  • 2021 Genome Biology - diffBUM-HMM a robust statistical modeling approach for detecting RNA flexibility changes in high-throughput structure probing data