Claude Scientific Skills

# ESM: Evolutionary Scale Modeling

Overview

ESM provides state-of-the-art protein language models for understanding, generating, and designing proteins. This skill enables working with two model families: ESM3 for generative protein design across sequence, structure, and function, and ESM C for efficient protein representation learning and embeddings.

Core Capabilities

1. Protein Sequence Generation with ESM3

Generate novel protein sequences with desired properties using multimodal generative modeling.

• When to use:
• Designing proteins with specific functional properties
• Completing partial protein sequences
• Generating variants of existing proteins
• Creating proteins with desired structural characteristics

Basic usage:

```python from esm.models.esm3 import ESM3 from esm.sdk.api import ESM3InferenceClient, ESMProtein, GenerationConfig

# Load model locally model: ESM3InferenceClient = ESM3.from_pretrained("esm3-sm-open-v1").to("cuda")

# Create protein prompt protein = ESMProtein(sequence="MPRT___KEND") # '_' represents masked positions

# Generate completion protein = model.generate(protein, GenerationConfig(track="sequence", num_steps=8)) print(protein.sequence) ```

For remote/cloud usage via Forge API:

```python from esm.sdk.forge import ESM3ForgeInferenceClient from esm.sdk.api import ESMProtein, GenerationConfig

# Connect to Forge model = ESM3ForgeInferenceClient(model="esm3-medium-2024-08", url="https://forge.evolutionaryscale.ai", token="<token>")

# Generate protein = model.generate(protein, GenerationConfig(track="sequence", num_steps=8)) ```

See `references/esm3-api.md` for detailed ESM3 model specifications, advanced generation configurations, and multimodal prompting examples.

2. Structure Prediction and Inverse Folding

Use ESM3's structure track for structure prediction from sequence or inverse folding (sequence design from structure).

Structure prediction:

```python from esm.sdk.api import ESM3InferenceClient, ESMProtein, GenerationConfig

# Predict structure from sequence protein = ESMProtein(sequence="MPRTKEINDAGLIVHSP...") protein_with_structure = model.generate( protein, GenerationConfig(track="structure", num_steps=protein.sequence.count("_")) )

# Access predicted structure coordinates = protein_with_structure.coordinates # 3D coordinates pdb_string = protein_with_structure.to_pdb() ```

Inverse folding (sequence from structure):

```python # Design sequence for a target structure protein_with_structure = ESMProtein.from_pdb("target_structure.pdb") protein_with_structure.sequence = None # Remove sequence

# Generate sequence that folds to this structure designed_protein = model.generate( protein_with_structure, GenerationConfig(track="sequence", num_steps=50, temperature=0.7) ) ```

3. Protein Embeddings with ESM C

Generate high-quality embeddings for downstream tasks like function prediction, classification, or similarity analysis.

• When to use:
• Extracting protein representations for machine learning
• Computing sequence similarities
• Feature extraction for protein classification
• Transfer learning for protein-related tasks

Basic usage:

```python from esm.models.esmc import ESMC from esm.sdk.api import ESMProtein

# Load ESM C model model = ESMC.from_pretrained("esmc-300m").to("cuda")

# Get embeddings protein = ESMProtein(sequence="MPRTKEINDAGLIVHSP...") protein_tensor = model.encode(protein)

# Generate embeddings embeddings = model.forward(protein_tensor) ```

Batch processing:

```python # Encode multiple proteins proteins = [ ESMProtein(sequence="MPRTKEIND..."), ESMProtein(sequence="AGLIVHSPQ..."), ESMProtein(sequence="KTEFLNDGR...") ]

embeddings_list = [model.logits(model.forward(model.encode(p))) for p in proteins] ```

See `references/esm-c-api.md` for ESM C model details, efficiency comparisons, and advanced embedding strategies.

4. Function Conditioning and Annotation

Use ESM3's function track to generate proteins with specific functional annotations or predict function from sequence.

Function-conditioned generation:

```python from esm.sdk.api import ESMProtein, FunctionAnnotation, GenerationConfig

# Create protein with desired function protein = ESMProtein( sequence="_" * 200, # Generate 200 residue protein function_annotations=[ FunctionAnnotation(label="fluorescent_protein", start=50, end=150) ] )

# Generate sequence with specified function functional_protein = model.generate( protein, GenerationConfig(track="sequence", num_steps=200) ) ```

5. Chain-of-Thought Generation

Iteratively refine protein designs using ESM3's chain-of-thought generation approach.

```python from esm.sdk.api import GenerationConfig

# Multi-step refinement protein = ESMProtein(sequence="MPRT" + "_" * 100 + "KEND")

# Step 1: Generate initial structure config = GenerationConfig(track="structure", num_steps=50) protein = model.generate(protein, config)

# Step 2: Refine sequence based on structure config = GenerationConfig(track="sequence", num_steps=50, temperature=0.5) protein = model.generate(protein, config)

# Step 3: Predict function config = GenerationConfig(track="function", num_steps=20) protein = model.generate(protein, config) ```

6. Batch Processing with Forge API

Process multiple proteins efficiently using Forge's async executor.

```python from esm.sdk.forge import ESM3ForgeInferenceClient import asyncio

client = ESM3ForgeInferenceClient(model="esm3-medium-2024-08", token="<token>")

# Async batch processing async def batch_generate(proteins_list): tasks = [ client.async_generate(protein, GenerationConfig(track="sequence")) for protein in proteins_list ] return await asyncio.gather(*tasks)

# Execute proteins = [ESMProtein(sequence=f"MPRT{'_' * 50}KEND") for _ in range(10)] results = asyncio.run(batch_generate(proteins)) ```

See `references/forge-api.md` for detailed Forge API documentation, authentication, rate limits, and batch processing patterns.

Model Selection Guide

• ESM3 Models (Generative):
• `esm3-sm-open-v1` (1.4B) - Open weights, local usage, good for experimentation
• `esm3-medium-2024-08` (7B) - Best balance of quality and speed (Forge only)
• `esm3-large-2024-03` (98B) - Highest quality, slower (Forge only)

• ESM C Models (Embeddings):
• `esmc-300m` (30 layers) - Lightweight, fast inference
• `esmc-600m` (36 layers) - Balanced performance
• `esmc-6b` (80 layers) - Maximum representation quality

• Selection criteria:
• Local development/testing: Use `esm3-sm-open-v1` or `esmc-300m`
• Production quality: Use `esm3-medium-2024-08` via Forge
• Maximum accuracy: Use `esm3-large-2024-03` or `esmc-6b`
• High throughput: Use Forge API with batch executor
• Cost optimization: Use smaller models, implement caching strategies

Installation

Basic installation:

```bash uv pip install esm ```

With Flash Attention (recommended for faster inference):

```bash uv pip install esm uv pip install flash-attn --no-build-isolation ```

For Forge API access:

```bash uv pip install esm # SDK includes Forge client ```

No additional dependencies needed. Obtain Forge API token at https://forge.evolutionaryscale.ai

Common Workflows

• For detailed examples and complete workflows, see `references/workflows.md` which includes:
• Novel GFP design with chain-of-thought
• Protein variant generation and screening
• Structure-based sequence optimization
• Function prediction pipelines
• Embedding-based clustering and analysis

References

This skill includes comprehensive reference documentation:

• `references/esm3-api.md` - ESM3 model architecture, API reference, generation parameters, and multimodal prompting
• `references/esm-c-api.md` - ESM C model details, embedding strategies, and performance optimization
• `references/forge-api.md` - Forge platform documentation, authentication, batch processing, and deployment
• `references/workflows.md` - Complete examples and common workflow patterns

These references contain detailed API specifications, parameter descriptions, and advanced usage patterns. Load them as needed for specific tasks.

Best Practices

• For generation tasks:
• Start with smaller models for prototyping (`esm3-sm-open-v1`)
• Use temperature parameter to control diversity (0.0 = deterministic, 1.0 = diverse)
• Implement iterative refinement with chain-of-thought for complex designs
• Validate generated sequences with structure prediction or wet-lab experiments

• For embedding tasks:
• Batch process sequences when possible for efficiency
• Cache embeddings for repeated analyses
• Normalize embeddings when computing similarities
• Use appropriate model size based on downstream task requirements

• For production deployment:
• Use Forge API for scalability and latest models
• Implement error handling and retry logic for API calls
• Monitor token usage and implement rate limiting
• Consider AWS SageMaker deployment for dedicated infrastructure

Resources and Documentation

• GitHub Repository: https://github.com/evolutionaryscale/esm
• Forge Platform: https://forge.evolutionaryscale.ai
• Scientific Paper: Hayes et al., Science (2025) - https://www.science.org/doi/10.1126/science.ads0018
• Blog Posts:
• - ESM3 Release: https://www.evolutionaryscale.ai/blog/esm3-release
• - ESM C Launch: https://www.evolutionaryscale.ai/blog/esm-cambrian
• Community: Slack community at https://bit.ly/3FKwcWd
• Model Weights: HuggingFace EvolutionaryScale organization

Responsible Use

ESM is designed for beneficial applications in protein engineering, drug discovery, and scientific research. Follow the Responsible Biodesign Framework (https://responsiblebiodesign.ai/) when designing novel proteins. Consider biosafety and ethical implications of protein designs before experimental validation.