---
title: ESMFold outputs and confidence
description: 'Read an ESMFold result — structure.pdb with pLDDT in the B-factor column plus pae.json — and what each pLDDT band supports, from above 90 down to below 50.'
---

ESMFold returns a predicted structure (`structure.pdb`) alongside per-residue pLDDT confidence scores and a PAE matrix. Read the pLDDT first: it tells you whether to trust the model for your next step — high-confidence cores (>90) are the only regions worth examining in detail, while low-confidence tails should be trimmed or masked before downstream docking or simulation. Note that even a high-confidence predicted receptor costs downstream accuracy: see [how ESMFold results compare to the bench](/docs/esmfold/translatability).

## Output artifacts

- **`structure.pdb`**: predicted 3D coordinates with pLDDT stored in the
  B-factor column (if enabled).
- **`pae.json` / `pae.png`**: per-residue predicted aligned error; helps assess
  domain placement.
- **`metadata.json`**: includes sequence, model version, and runtime parameters.

## Understanding pLDDT confidence scores

pLDDT (predicted Local Distance Difference Test) is a per-residue confidence metric that ESMFold provides for each amino acid in the predicted structure. The score ranges from 0 to 100 and indicates how confident the model is in the local structure around each residue. This metric is derived from the ESM-2 language model's internal representations and correlates well with the actual accuracy of the predicted coordinates.

### pLDDT score interpretation

- **90–100**: Very high confidence. On the CAMEO test set, ESMFold predictions above this threshold had a median all-atom RMSD<sub>95</sub> of 1.42 Å and backbone RMSD<sub>95</sub> of 0.94 Å against the experimental structure (author-reported). These regions are the ones worth using for detailed structural analysis and mechanistic reasoning — but docking into a predicted receptor still costs accuracy relative to a crystal structure.
- **70–90**: Confident prediction. Backbone geometry is generally reliable, but side-chain rotamers may vary. Suitable for most structural biology applications with appropriate caution.
- **50–70**: Low confidence. Treat these regions as provisional. Often corresponds to flexible loops, surface-exposed regions, or areas with limited structural constraints. Use for general topology only.
- **&lt;50**: Very low confidence. These regions are likely intrinsically disordered or unstructured. Do not rely on the predicted geometry. Consider these regions as placeholders rather than accurate predictions.

### Using pLDDT for quality assessment

- **Mean pLDDT**: A useful summary metric; values above 70 generally indicate a reliable overall fold
- **pLDDT distribution**: Examine the per-residue plot to identify confident cores vs. flexible regions
- **Domain identification**: Sharp transitions in pLDDT can indicate domain boundaries
- **Comparison with known structures**: High pLDDT regions should align well with experimental structures when available

## Interpreting PAE

- Low PAE between domains suggests stable relative placement.
- High off-diagonal PAE indicates uncertain domain orientation; domain splitting
  may be needed.

## Quality checks

- Inspect pLDDT coloring in a viewer; focus on high-confidence cores.
- Trim or mask low-confidence tails before downstream docking or simulation.
- Validate secondary structure plausibility with external tools if pLDDT is
  marginal.

## Canvas Visualization

When an ESMFold job completes, a result card appears on the canvas.

- **Card size**: 450×560px
- **Border color**: Green (#4CAF50)
- **Visualization**: Interactive 3D Mol* viewer with rotate, zoom, and pan

### What You See

- pLDDT score (0–100) with confidence category
- pTM score (structure-level metric)
- Residue count
- Color modes: confidence (pLDDT), chain, secondary structure, hydrophobicity
- Representation modes: cartoon, ball-and-stick, surface
- Sequence bar with residue highlighting

### Interpreting Canvas Metrics

| Metric | Good Value | Concern |
|--------|-----------|---------|
| pLDDT &gt; 90 | Very high confidence — median all-atom RMSD<sub>95</sub> 1.42 Å on CAMEO | A predicted receptor still costs pose accuracy downstream |
| pLDDT 70–90 | Confident — backbone reliable | Side-chain rotamers may vary |
| pLDDT 50–70 | Low confidence — general topology only | Loops and flexible regions |
| pLDDT &lt; 50 | Very low — likely disordered | Do not use for detailed analysis |

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