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esm

Generate protein sequences and embeddings using ESM3 and ESM C.

Updated Mar 10, 2026
Search Tags:#embeddings#bioinformatics#esm#structure prediction#protein design#generative models#protein language models
One-click install
npx skills add https://github.com/Yezez9/Research-Agent --skill esm-yezez9
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: esm
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/esm
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill esm-yezez9

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides a comprehensive toolkit for working with advanced protein language models, enabling complex tasks like protein design, structure prediction, and function analysis that were previously intractable.

Core Features & Use Cases

  • Generative Protein Design: Design novel protein sequences and structures with desired functions using ESM3.
  • Protein Embeddings: Generate high-quality embeddings for downstream tasks like classification and clustering using ESM C.
  • Structure Prediction & Inverse Folding: Predict 3D protein structures from sequences or design sequences from target structures.
  • Use Case: A researcher needs to design a new enzyme with specific catalytic activity. They can use ESM3 to generate candidate sequences and structures, then use ESM C embeddings to predict their functional properties and select the most promising candidates.

Quick Start

Use the esm skill to generate a protein sequence for the prompt 'MPRT___KEND'.

Frequently Asked Questions about esm

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

FAQPage Schema
How do I generate protein embeddings for downstream machine learning tasks?▼

Generate protein embeddings by inputting amino acid sequences into ESM C. This produces high-quality vector representations for downstream classification and clustering tasks.

Can I design novel protein sequences with specific functions using generative models?▼

Design novel protein sequences with specific functions using ESM3. This generative model facilitates protein sequence generation and structure prediction for targeted catalytic activity.

What is the best way to predict 3D protein structures from amino acid sequences?▼

Predict 3D protein structures from sequences using this toolkit's ESM3 capabilities. It enables accurate structure prediction alongside inverse folding to design sequences from target structures.

Does the esm skill support local model execution for protein analysis?▼

The esm skill supports local model execution for protein analysis. It also facilitates cloud-based inference via the Forge API to provide scalable solutions for complex bioinformatics tasks.

How do I perform inverse folding to design protein sequences from target structures?▼

Perform inverse folding by providing target 3D structures to the ESM3 model. It designs corresponding amino acid sequences that fold into the desired structural conformations for functional annotation.

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