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RNA 3D Structure Prediction

Note

  • Autoregressive Approach:
    • AlphaFold 2, Nature, 2021
    • RoseTTAFold2, bioRxiv, 2023
  • Diffusion Approach:
    • RFDiffusion, Nature, 2023
    • RoseTTAFold All-Atom, Science, 2024
    • AlphaFold 3 (All-Atom), Nature, 2024

0. Protein Tertiary Structure Prediction

Learn from Protein structure prediction

  • All Atom Models
  • ✅ 2024 Nature - Accurate structure prediction of biomolecular interactions with AlphaFold 3
  • ✅ 2024 Science - Generalized biomolecular modeling and design with RoseTTAFold All-Atom
  • ✅ 2024 Nature - Conformational ensembles of the human intrinsically disordered proteome
  • 2021 Nature – AlphaFold2: Highly accurate protein structure prediction with AlphaFold
  • 2017 Science - Protein structure determination using metagenome sequence data

1. RNA Tertiary Structure Prediction

  • 2022 PNAS - Thoughts on how to think (and talk) about RNA structure
  • 2022 bioRxiv - Accurate de novo prediction of RNA 3D structure with transformer network
  • 2022 bioRxiv - DeepFoldRNA: De Novo RNA Tertiary Structure Prediction at Atomic Resolution using Geometric Potentials from Deep Learning
  • 2022 arxiv - E2Efold-3D: End-to-End Deep Learning Method for accurate de novo RNA 3D Structure Prediction
  • 2022 bioRxiv - Accurate prediction of nucleic acid and protein-nucleic acid complexes using RoseTTAFoldNA
  • ✅ 2021 Science - ARES: Geometric deep learning of RNA structure
  • [Graphical Modeling] 2021 Methods Mol Biol - Modeling and Predicting RNA Three-Dimensional Structures