ESM2 Protein Language Model
Prerequisites
| Requirement | Minimum | Recommended |
|---|---|---|
| Python | 3.8+ | 3.10 |
| PyTorch | 1.10+ | 2.0+ |
| CUDA | 11.0+ | 11.7+ |
| GPU VRAM | 8GB | 24GB (A10G) |
| RAM | 16GB | 32GB |
How to run
First time? See Installation Guide to set up Modal and biomodals.
Option 1: Modal
cd biomodals
modal run modal_esm2_predict_masked.py \
--input-faa sequences.fasta \
--out-dir embeddings/GPU: A10G (24GB) | Timeout: 300s default
Option 2: Python API (recommended)
import torch
import esm
# Load model
model, alphabet = esm.pretrained.esm2_t33_650M_UR50D()
batch_converter = alphabet.get_batch_converter()
model = model.eval().cuda()
# Process sequences
data = [("seq1", "MKTAYIAKQRQISFVK...")]
batch_labels, batch_strs, batch_tokens = batch_converter(data)
with torch.no_grad():
results = model(batch_tokens.cuda(), repr_layers=[33])
# Get embeddings
embeddings = results["representations"][33]Key parameters
ESM2 Models
| Model | Parameters | Speed | Quality |
|---|---|---|---|
| esm2_t6_8M | 8M | Fastest | Fast screening |
| esm2_t12_35M | 35M | Fast | Good |
| esm2_t33_650M | 650M | Medium | Better |
| esm2_t36_3B | 3B | Slow | Best |
Output format
embeddings/
├── embeddings.npy # (N, 1280) array
├── pll_scores.csv # PLL for each sequence
└── metadata.json # Sequence infoSample output
Successful run
$ modal run modal_esm2_predict_masked.py --input-faa designs.fasta
[INFO] Loading ESM2-650M model...
[INFO] Processing 100 sequences...
[INFO] Computing pseudo-log-likelihood...
embeddings/pll_scores.csv:
sequence_id,pll,pll_normalized,length
design_0,-0.82,0.15,78
design_1,-0.95,0.08,85
design_2,-1.23,-0.12,72
...
Summary:
Mean PLL: -0.91
Sequences with PLL > 0: 42/100 (42%)What good output looks like:
- PLL_normalized: > 0.0 (more natural-like)
- Embeddings shape: (N, 1280) for 650M model
- Higher PLL = more natural sequence
Decision tree
Should I use ESM2?
│
├─ What do you need?
│ ├─ Sequence plausibility score → ESM2 PLL ✓
│ ├─ Embeddings for clustering → ESM2 ✓
│ ├─ Variant effect prediction → ESM2 ✓
│ └─ Structure prediction → Use ESMFold
│
├─ What model size?
│ ├─ Fast screening → esm2_t12_35M
│ ├─ Standard use → esm2_t33_650M ✓
│ └─ Best quality → esm2_t36_3B
│
└─ Use case?
├─ QC filtering → PLL > 0.0 threshold
├─ Diversity analysis → Mean-pooled embeddings
└─ Mutation scanning → Per-position log-oddsPLL interpretation
| Normalized PLL | Interpretation |
|---|---|
| > 0.2 | Very natural sequence |
| 0.0 - 0.2 | Good, natural-like |
| -0.5 - 0.0 | Acceptable |
| < -0.5 | May be unnatural |
Typical performance
| Campaign Size | Time (A10G) | Cost (Modal) | Notes |
|---|---|---|---|
| 100 sequences | 5-10 min | ~$1 | Quick screen |
| 1000 sequences | 30-60 min | ~$5 | Standard |
| 5000 sequences | 2-3h | ~$20 | Large batch |
Throughput: ~100-200 sequences/minute with 650M model.
Verify
wc -l embeddings/pll_scores.csv # Should match input + 1 (header)Troubleshooting
OOM errors: Use smaller model or batch sequences Slow processing: Use esm2_t12_35M for speed Low PLL scores: May indicate unusual/designed sequences
Error interpretation
| Error | Cause | Fix |
|---|---|---|
RuntimeError: CUDA out of memory | Sequence too long or large batch | Reduce batch size |
KeyError: representation | Wrong layer requested | Use layer 33 for 650M model |
ValueError: sequence | Invalid amino acid | Check for non-standard AAs |
Next: Structure prediction with chai or boltz → protein-qc for filtering.