ArticleNature methods2024
Accurate prediction of protein-nucleic acid complexes using RoseTTAFoldNA.
Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 229 papers, 1 of them a synthesis that pooled it.
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Who cites it
229 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Advances in the Application of Protein Language Modeling for Nucleic Acid Protein Binding Site Prediction.Genes · 2024Pooled it
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- dsRNAscan maps human dsRNAome, revealing conservation, intermolecular dsRNA, and correlates of ADAR dependency.Molecular cell · 2026Article
- The MODNAP benchmark set for modeling ribose-based modified nucleic acid and nucleic acid-protein complexes: a case study with AlphaFold 3.Nucleic acids research · 2026Article
- The trRosettaRNA server for RNA structure prediction.Nature protocols · 2026Review
- The Advantages of AI for Computational Protein Studies and Looking Ahead at the Next Challenges: Single Structures Are Not Enough.Journal of molecular biology · 2026Review
- Building RNA coarse-grained force fields: Design principles and training strategies.Biophysical journal · 2026Review
- Reimagining computational macromolecular modeling: AI-driven approaches.Biophysical journal · 2026Review
- Dockground: Expanding the Resource to Protein-DNA Complexes.Journal of molecular biology · 2026Article
- Upcycling Vegetable Waste Into Functional Food Ingredients via Synergistic Microbial Engineering and Artificial Intelligence.Comprehensive reviews in food science and food safety · 2026Review
- Limits of deep-learning-based RNA prediction methods.Nucleic acids research · 2026Article
- Identification of methylation-sensitive human transcription factors using meSMiLE-seq.Nature communications · 2026Article
- Article
- Opportunities for artificial intelligence and synthetic biology in designing living drug delivery systems.Advanced drug delivery reviews · 2026Review
- SoPPIs: a highly parallelized protein-protein-interaction screening method in prokaryotic and eukaryotic hosts.Nucleic acids research · 2026Article
- Conformational analysis of nucleic acids for optimizing DNA and RNA topological models.Nucleic acids research · 2026Article
- A brief guideline for the studies of structure-function relationship of ion channels using AlphaFold3.Fundamental research · 2026Review
- RNAbpFlow: base pair-augmented SE(3) flow matching for conditional RNA 3D structure generation.Nature methods · 2026Article
- A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function.Nature biotechnology · 2026Article
- A protocol for single-sequence protein-RNA complex structure prediction using ProRNA3D-single.STAR protocols · 2026Article
169 more citing papers are in PubMed but not listed here.
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6 authors.
Funding
Abstract
Protein-RNA and protein-DNA complexes play critical roles in biology. Despite considerable recent advances in protein structure prediction, the prediction of the structures of protein-nucleic acid complexes without homology to known complexes is a largely unsolved problem. Here we extend the RoseTTAFold machine learning protein-structure-prediction approach to additionally predict nucleic acid and protein-nucleic acid complexes. We develop a single trained network, RoseTTAFoldNA, that rapidly produces three-dimensional structure models with confidence estimates for protein-DNA and protein-RNA complexes. Here we show that confident predictions have considerably higher accuracy than current state-of-the-art methods. RoseTTAFoldNA should be broadly useful for modeling the structure of naturally occurring protein-nucleic acid complexes, and for designing sequence-specific RNA and DNA-binding proteins.
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