# ESMfold MCP Server

> Use this tool when you need to analyze protein sequences and predict structures at scale, as it solves problems in bioinformatics by extracting embeddings and processing large batches of FASTA files. The ESMfold MCP Server takes in FASTA files as input and outputs predicted protein structures, utilizing a Docker-based interface for efficient batch processing. It is ideal for large-scale protein analysis and structure prediction tasks that require high-performance computing and model management.

Canonical page: https://skillsregistry.net/skills/macromnex-esmfold-mcp  
JSON: https://api.skillsregistry.net/v1/skills/macromnex-esmfold-mcp

## Description

Enables protein sequence analysis and structure prediction by extracting ESM-2 embeddings and batch processing FASTA files via Docker. It provides tools for large-scale embedding extraction, job monitoring, and model management within an MCP-compatible environment.

## Trust

- **Trust score (0–1):** 0.87
- **Verification tier:** verified
- **Last scanned:** 2026-09-19

## Facts

- **Version:** 1.0.0
- **Skill type:** atomic
- **Execution layer:** mcp-remote
- **Runtime environment:** api
- **Category:** cloud-infra
- **Updated:** 2026-09-19

## Source

- **Source listing:** [Glama](https://glama.ai/mcp/servers/dehs6ezbre)
- **Repository:** <https://github.com/MacromNex/esmfold_mcp>

## Use it

Resolve this record through the SkillsRegistry MCP server (no auth, read-only):

```
claude mcp add --transport http --scope user skillsregistry https://api.skillsregistry.net/mcp
```

```json
{
  "jsonrpc": "2.0",
  "id": 1,
  "method": "tools/call",
  "params": {
    "name": "get_skill",
    "arguments": {
      "slug": "macromnex-esmfold-mcp"
    }
  }
}
```

REST: `GET https://api.skillsregistry.net/v1/skills/macromnex-esmfold-mcp` · pull for local use: `GET https://api.skillsregistry.net/v1/skills/macromnex-esmfold-mcp/pull`

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SkillsRegistry indexes agent skills from public registries and GitHub. Skills we have analysed are scanned with Circle-IR and scored on six dimensions; each listing states its scan coverage. More: https://skillsregistry.net/llms.txt