AlphaFold 3 RNA Structure & RBP Binding Predictor
This protocol predicts RNA secondary and tertiary structures using AlphaFold 3, with extension to RNA-protein complex prediction for RNA-binding proteins. The workflow identifies structured regions, disordered regions, and potential RBP binding interfaces, supporting research on non-coding RNA function and post-transcriptional regulation.
AlphaFold 3 RNA Structure & RBP Binding Predictor
Abstract
This protocol predicts RNA structures and RNA-protein complexes using AlphaFold 3, supporting research on non-coding RNA function.
Motivation
RNA structure is fundamental to splicing, translation regulation, and cellular defense. Key challenges:
- RNA structure is dynamic and context-dependent
- Many RNAs are partially disordered
- RBP binding sites are often in flexible regions
Our protocol provides RNA 3D structure prediction, confidence mapping, and RBP binding interface prediction.
Methodology
Confidence Interpretation
| pLDDT Range | Interpretation |
|---|---|
| > 90 | Very high confidence - canonical helix |
| 70-90 | Confident - structured region |
| 50-70 | Low confidence - flexible/loop |
| < 50 | Very low - intrinsically disordered |
RBP Binding Analysis
For RNA-protein complexes, predict the binary complex and extract interface metrics.
Key RBP domains modeled: RRM, KH domain, RGG box, ZnF (CCHC).
Expected Outcomes
- Structured regions: High pLDDT (> 70)
- Loops/junctions: Moderate pLDDT (50-70)
- Disordered tails: Low pLDDT (< 50)
Limitations
- Pseudoknots not well modeled
- Modified nucleotides not supported
- Does not predict folding kinetics
References
- Dawson & Pettitt, Nuc Acid Res, 2024
- Abramson et al., Nature, 2024
Reproducibility: Skill File
Use this skill file to reproduce the research with an AI agent.
--- name: alphafold3-rna-rbp-protocol description: Predict RNA secondary structure and RNA-protein binding interfaces using AlphaFold 3. allowed-tools: WebFetch, Bash(python *), Bash(mkdir *), Bash(cp *), Bash(ls *), Bash(jq *), Bash(cd *) --- # AlphaFold 3 RNA Structure & RBP Binding Predictor Protocol ## Purpose Predict RNA secondary and tertiary structure, and analyze RNA-binding protein (RBP) interaction interfaces. ## Inputs - `inputs/rna.json` or `inputs/rna.fasta`: RNA sequence(s). - `inputs/rbp.json` (optional): RNA-binding protein for binding prediction. - `inputs/metadata.md`: RNA type, organism source. ## Pre-Run Checks 1. Confirm research use is permitted. 2. Validate RNA sequence uses only A, U, G, C. 3. Check for potential pseudoknots. 4. Verify sequence length is appropriate. ## Step 1: RNA Structure Prediction Run AlphaFold 3 prediction for the RNA. ## Step 2: Analyze RNA Structure Extract pLDDT scores, identify base pairing, and distinguish structured vs disordered regions. ## Step 3: Predict RBP Binding (if applicable) Prepare RNA-protein complex input and predict binding interface. ## Step 4: Analyze RBP Binding Interface Extract binding metrics including interface residues and confidence. ## Step 5: Motif Analysis Identify known RNA-binding motifs in the protein. ## Success Criteria - RNA structure is predicted with interpretable confidence. - Structural elements are identified. - Report provides testable hypotheses. ## Failure Modes - RNA prediction fails → check for invalid characters - Very low pLDDT throughout → RNA may be highly flexible ## References - AlphaFold 3: Abramson et al., Nature, 2024
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