Use JapanFold in Claude¶

JapanFold works in every Claude product. Pick the one you use; each block is the whole setup.

There are two ways in, and they combine. The connector gives Claude JapanFold's tools and signs you in in the browser, so there is no key to copy. The skill teaches Claude every model and input shape, and calls the API with your key. A new account starts with $100.00 of credit either way.

claude.ai, Claude Desktop and mobile¶

Connect to Claude

The button opens claude.ai with the connector filled in. Check the name and URL and select Add. To do it by hand:

In claude.ai, open Customize > Connectors, select + Add, then Add custom connector. In Claude Desktop, Customize is in the sidebar.
Name it JapanFold and enter the URL https://api.japanfold.aiand.com/mcp.
Select Connect and sign in with your email address when the browser opens.

A connector added on the web or on Desktop is also there in the Claude mobile app, so add it on a computer first. On the Free plan you can add one custom connector. On Team and Enterprise, an Owner adds it for everyone under Organization settings > Connectors (prefilled link), and each member then connects with their own account.

Then ask, for example: "Fold MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQ with Boltz-2 and tell me how confident it is." The connector shows up under API keys on your account page; revoking it there disconnects it.

Claude Code¶

Set your key in the terminal you start Claude Code from (make one at japanfold.aiand.com/account/token):

export JAPANFOLD_API_KEY=jf_live_your_token

Then install the plugin, which carries the skill and updates with /plugin marketplace update:

/plugin install japanfold --marketplace japanfold/japanfold

That one-step form needs Claude Code 2.1.275 or later. On an older version, run /plugin marketplace add japanfold/japanfold and then /plugin install japanfold@japanfold. Restart Claude Code and ask it to fold or design.

To use the tools instead of (or beside) the skill, add the MCP server:

claude mcp add --transport http japanfold https://api.japanfold.aiand.com/mcp \
  --header "Authorization: Bearer $JAPANFOLD_API_KEY"

Without the header, claude mcp login japanfold signs you in in the browser instead. Other ways to install the skill, including npx skills for Cursor, Codex and Gemini CLI, are on The JapanFold skill.

Claude Science¶

Claude Science takes both the connector and the skill.

Connector. If you already connected JapanFold in claude.ai, it is listed under Settings > Connectors and you are done. Otherwise go to Settings > Connectors > Add connector, choose Remote, name it japanfold, enter https://api.japanfold.aiand.com/mcp and sign in when asked.
Skill. Go to Settings > Skills > Add skill > Import from GitHub and enter japanfold/japanfold. An imported skill does not update by itself: to pick up new models, open Imported, then the menu next to the repository, and select Check for updates….

Claude asks before it calls a JapanFold tool the first time, and before its code reaches api.japanfold.aiand.com. On Team and Enterprise plans, custom connectors and skills work only if your organization allows them.

Claude API¶

The Messages API connects to the MCP server itself. Pass your JapanFold key as the authorization_token:

import os
import anthropic

client = anthropic.Anthropic()
response = client.beta.messages.create(
    model="claude-opus-5-5",
    max_tokens=4096,
    messages=[{"role": "user", "content":
               "Fold MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQ with ESMFold-2 and report the pLDDT."}],
    mcp_servers=[{"type": "url", "url": "https://api.japanfold.aiand.com/mcp", "name": "japanfold",
                  "authorization_token": os.environ["JAPANFOLD_API_KEY"]}],
    tools=[{"type": "mcp_toolset", "mcp_server_name": "japanfold"}],
    betas=["mcp-client-2025-11-20"],
)

Claude submits the job and follows it with get_job, which holds for up to 100 s a call. Anthropic's MCP connector guide covers the rest.

Claude Agent SDK¶

The Agent SDK runs that loop for you. Register the server over HTTP with your key, and allow its tools:

import os
from claude_agent_sdk import ClaudeAgentOptions, query

options = ClaudeAgentOptions(
    mcp_servers={"japanfold": {
        "type": "http",
        "url": "https://api.japanfold.aiand.com/mcp",
        "headers": {"Authorization": f"Bearer {os.environ['JAPANFOLD_API_KEY']}"},
    }},
    allowed_tools=["mcp__japanfold__*"],
)

async for message in query(prompt="Fold MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQ with Boltz-2.", options=options):
    print(message)

In TypeScript the option is mcpServers, with the same fields. See Anthropic's Agent SDK MCP guide.