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esm

Generate and analyze protein sequences, structures, and functions with ESM3 and ESM C models.

4|1|Updated Jun 18, 2025
Search Tags:#embeddings#esm#protein-design#structure-prediction#forge-api#protein-language-models
One-click install
npx skills add https://github.com/HolobiomicsLab/Toolomics --skill esm-holobiomicslab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: esm
Source: https://github.com/HolobiomicsLab/Toolomics/tree/main/mcp_host/skills/scientific-skills/scientific-skills/esm
Command: npx skills add https://github.com/HolobiomicsLab/Toolomics --skill esm-holobiomicslab

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Protein design, embedding, and analysis at scale using ESM3 and ESM C models. Enable researchers to prototype novel proteins, compute embeddings for large datasets, and perform structure-guided design locally or via Forge.

Core Features & Use Cases

  • Multimodal protein generation and analysis across sequence, structure, and function.
  • Local and Forge API access for scalable inference and experiments.
  • Embedding extraction, inverse folding, and function conditioning for research and development.

Quick Start

Load a pretrained ESM3 model and start generating sequences, predicting structures, or obtaining embeddings.

Frequently Asked Questions about esm

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I generate and analyze novel protein sequences using ESM models?▼

You can generate and analyze novel protein sequences by loading pretrained ESM3 or ESM C models to perform multimodal generation, inverse folding, and function conditioning for research and development.

Can I compute protein embeddings for large datasets via the Forge API?▼

Yes, you can compute protein embeddings for large datasets by accessing ESM3 and ESM C models via the Forge API, enabling scalable inference and experiments without local hardware constraints.

Do I need GPU acceleration for structure prediction with protein language models?▼

GPU acceleration is highly recommended for optimal performance when running structure prediction and embedding extraction with ESM models, especially when handling large datasets or executing complex multimodal analyses locally.

What is the best way to perform structure-guided protein design locally?▼

The best way to perform structure-guided protein design locally is by using the esm package with ESM3 models to execute multimodal protein generation, inverse folding, and sequence analysis directly on your hardware.

Does ESM3 support function conditioning for protein design?▼

Yes, ESM3 supports function conditioning, allowing researchers to guide the multimodal protein generation process by specifying desired functional constraints alongside sequence and structure inputs.

What are the limitations of running large ESM models without Forge access?▼

Without Forge access, running large ESM models locally requires significant GPU resources to handle the computational load, which may limit the scale of embedding extraction, structure prediction, and protein design experiments.

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