API Documentation

MCP Server

Tamarind offers a Model Context Protocol (MCP) server that allows AI assistants and other applications to access Tamarind's computational biology tools. With the MCP server, you can:

  • Submit jobs for any tool on Tamarind, including structure prediction, protein design, docking, and more
  • Query job status and retrieve results
  • Upload and manage input files
  • Access all Tamarind tools through natural language

Example prompts you can use with your AI assistant:

  • "Submit an RFDiffusion job to design a binder for this target protein"
  • "Check the status of my recent structure prediction jobs"
  • "Get the results from my batch antibody design job"
Requirements

To use Tamarind's MCP server, you need:

  1. A Tamarind account - Sign up here
  2. OAuth credentials (see OAuth 2.1 below) or an API key - Get yours at API Key or email info@tamarind.bio
  3. A compatible MCP client - Such as Claude.ai, Claude Code, VS Code, Codex, or other MCP-compatible tools
Authentication

Tamarind MCP server supports two authentication methods:

OAuth 2.1

OAuth authentication provides user-specific access control and is the recommended method for most users.

Client ID: V8apuKVjc88f0FNP

Client Secret: Sign in to view

Authorization URL: https://clerk.tamarind.bio/oauth/authorize

Token URL: https://clerk.tamarind.bio/oauth/token

Enterprise gateways and custom MCP clients often use their own OAuth callback URL. If you see a redirect_uri mismatch error, submit the exact URI your client sends and we will add it to our OAuth allowlist.

Sign in to request a redirect URI registration.

API Key

API key authentication is a simpler alternative suitable for personal use or automation. Pass your API key via the x-api-key header. View your API key at API Key or email info@tamarind.bio to request access.

Server URL: https://mcp.tamarind.bio/mcp

Client Setup Instructions

Claude.ai provides the simplest way to connect to Tamarind's MCP server with no installation required.

Prerequisites

  • Claude.ai account (free or paid)

Setup Steps

  1. Go to claude.ai
  2. Click on your profile icon → Settings
  3. Navigate to Connectors
  4. Click Add custom connector
  5. Fill in the connector details:
    • Name: Tamarind
    • Remote MCP server URL: https://mcp.tamarind.bio/mcp
  6. Expand Advanced settings and enter your Tamarind OAuth credentials (both required):
    • OAuth Client ID: V8apuKVjc88f0FNP
    • OAuth Client Secret: See the Client Secret in the Authentication section above
  7. Click Add
  8. You'll be redirected to sign in with your Tamarind account and authorize the connection

Once connected, you can use Tamarind tools directly in your Claude.ai conversations!

Uploading files? Large files are streamed to mcp.tamarind.bio with a curl command. This client's sandbox blocks outbound network by default, so the upload fails with "network unreachable" until you allow the domain: open Settings → Capabilities, enable Allow network egress, and add mcp.tamarind.bio under Additional allowed domains. Connecting the MCP server itself does not need this - only the upload curl does. (Files ≤ 4 MB can be uploaded inline without it.)

Add the Tamarind MCP server directly from the command line:

1claude mcp add --transport http tamarind https://mcp.tamarind.bio/mcp \
2  --header "x-api-key:YOUR_API_KEY_HERE"

Replace YOUR_API_KEY_HERE with your API key, then restart Claude Code.

Add Tamarind from the Connectors UI, or edit the configuration file directly.

Connectors UI (recommended)

The same four values used on Claude.ai:

  1. Open Settings → Connectors
  2. Click Add → Add custom connector
  3. Fill in the connector details:
    • Name: Tamarind
    • Remote MCP server URL: https://mcp.tamarind.bio/mcp
  4. Expand Advanced settings and enter your Tamarind OAuth credentials (both required):
    • OAuth Client ID: V8apuKVjc88f0FNP
    • OAuth Client Secret: See the Client Secret in the Authentication section above
  5. Click Add
  6. Sign in with your Tamarind account to authorize the connection

Tamarind then appears in your connectors list, and its tools are available in new conversations.

API Key Authentication (config file)

  1. Get your API key from API Key
  2. Open your Claude Desktop configuration file:
    • macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
    • Windows: %APPDATA%\Claude\claude_desktop_config.json
  3. Add the Tamarind MCP server configuration:
1{
2  "mcpServers": {
3    "tamarind": {
4      "command": "npx",
5      "args": [
6        "mcp-remote",
7        "https://mcp.tamarind.bio/mcp",
8        "--header",
9        "x-api-key:YOUR_API_KEY_HERE"
10      ]
11    }
12  }
13}

Replace YOUR_API_KEY_HERE with your API key, then restart Claude Desktop.

OAuth Authentication (config file)

  1. Get your OAuth credentials from the Authentication section above
  2. Open your Claude Desktop configuration file:
    • macOS: ~/Library/Application Support/Claude/claude_desktop_config.json
    • Windows: %APPDATA%\Claude\claude_desktop_config.json
  3. Add the Tamarind MCP server configuration (see below)
  4. Restart Claude Desktop
  5. The first time you use Tamarind tools, you'll be prompted to authenticate in your browser
  6. Log in with your Tamarind account
1{
2  "mcpServers": {
3    "tamarind": {
4      "command": "npx",
5      "args": [
6        "mcp-remote",
7        "https://mcp.tamarind.bio/mcp",
8        "3334",
9        "--static-oauth-client-info",
10        "{\"client_id\":\"V8apuKVjc88f0FNP\",\"client_secret\":\"YOUR_CLIENT_SECRET\"}"
11      ]
12    }
13  }
14}

Replace YOUR_CLIENT_SECRET with your client secret (revealed in the Authentication section above), then restart Claude Desktop. Once connected, you'll see Tamarind appear in your connectors list.

Uploading files? Large files are streamed to mcp.tamarind.bio with a curl command. This client's sandbox blocks outbound network by default, so the upload fails with "network unreachable" until you allow the domain: open Settings → Capabilities, enable Allow network egress, and add mcp.tamarind.bio under Additional allowed domains. Connecting the MCP server itself does not need this - only the upload curl does. (Files ≤ 4 MB can be uploaded inline without it.)

Claude Science registers its own OAuth client, so there are no credentials to paste - leave Advanced settings empty.

Setup Steps

  1. Open Settings → Connectors
  2. Click Add connector → Remote URL
  3. Fill in the connector details:
    • Name: Tamarind
    • Remote MCP server URL: https://mcp.tamarind.bio/mcp
  4. Click Add
  5. Click Connect, then sign in with your Tamarind account to authorize the connection

Tamarind then appears under Custom in your connectors list, and its tools are available in new conversations.

Connect using API

To set it up, add your API key:

  1. Open Settings → Credentials → Add
  2. Set Name to TAMARIND_API_KEY
  3. Set Value to your API key, copied from API Key

VS Code supports MCP servers through GitHub Copilot Chat. Add the following to .vscode/mcp.json in your workspace (or use Cmd+Shift+P → "MCP: Add Server"):

1{
2  "servers": {
3    "tamarind": {
4      "type": "http",
5      "url": "https://mcp.tamarind.bio/mcp",
6      "headers": {
7        "x-api-key": "${input:tamarind-api-key}"
8      }
9    }
10  },
11  "inputs": [
12    {
13      "type": "promptString",
14      "id": "tamarind-api-key",
15      "description": "Tamarind API Key",
16      "password": true
17    }
18  ]
19}

VS Code will prompt you for the API key on first use. You can then use @tamarind in Copilot Chat to access Tamarind tools.

Refer to the VS Code MCP documentation for more details.

Tamarind Bio is published in the ChatGPT plugin directory. No configuration, API key, or installation is required.

  1. Go to chatgpt.com
  2. Open Plugins
  3. Search for Tamarind Bio
  4. Click Install
  5. Sign in with your Tamarind account when prompted to authorize the connection

Once connected, Tamarind tools are available directly in your ChatGPT conversations.

Install the published Tamarind Bio plugin in the Codex desktop app. Adding the server by hand is only needed if you installed our plugin repository as a marketplace instead.

Install the plugin (recommended)

  1. Open Plugins in the Codex sidebar
  2. Search for Tamarind Bio
  3. Click Install and complete the authorization prompt

The plugin brings the MCP server and all Tamarind skills with it. Nothing else to configure.

Add the server manually

Use this if you added Tamarind-Bio/tamarind-agent-plugin as a plugin marketplace. That install registers the server, so tamarind appears under MCPs → From plugins, but the entry carries no credentials and its Authenticate button will not connect it. Connect it with an API key instead:

  1. Get your API key from API Key
  2. Open Settings → Plugins → MCPs → Add server
  3. Set Name to tamarind
  4. Set Type to Streamable HTTP (the STDIO default is for local servers and will not connect)
  5. Set URL to https://mcp.tamarind.bio/mcp
  6. Under Headers, add x-api-key with your API key as the value
  7. Save, then start a new task so Codex discovers the tools

Codex CLI

  1. Set your API key as an environment variable in your shell profile (~/.zshrc or ~/.bashrc):
1export TAMARIND_API_KEY="your-api-key-here"
  1. Add the following to ~/.codex/config.toml:
1[mcp_servers.tamarind]
2url = "https://mcp.tamarind.bio/mcp"
3env_http_headers = { "x-api-key" = "TAMARIND_API_KEY" }
  1. Launch Codex and use Tamarind tools directly

Antigravity connects with the OAuth credentials above. Add the server to its MCP config, then authorize in the browser - there is nothing to paste back into the editor.

  1. Open Settings → Installed MCP Servers and click Open MCP Config
  2. Add the Tamarind server:
1{
2  "mcpServers": {
3    "tamarind": {
4      "serverUrl": "https://mcp.tamarind.bio/mcp",
5      "oauth": {
6        "clientId": "V8apuKVjc88f0FNP",
7        "clientSecret": "YOUR_CLIENT_SECRET"
8      }
9    }
10  }
11}
  1. Replace YOUR_CLIENT_SECRET with the Client Secret from the Authentication section above, then save the file
  2. Back in Installed MCP Servers, click Authenticate next to tamarind
  3. Sign in with your Tamarind account to authorize the connection

Until you authorize, the server shows Error: calling "initialize": Unauthorized. That is expected - it means Antigravity has the server but no token yet, and it clears once Authenticate completes.

Any MCP-compatible client (Cursor, Windsurf, or custom implementations) can connect to the Tamarind MCP server at https://mcp.tamarind.bio/mcp using API key authentication. Pass your key via the x-api-key header.

Refer to your specific client's documentation for configuration details. If you need help, email info@tamarind.bio.

Available Tools

The Tamarind MCP server exposes 30 tools. Expand any tool to see its parameters. Each tool declares whether it only reads data or may modify it, so your MCP client can flag writes before running them.

Read-only - Safe queries that never modify your data.
ParameterTypeRequiredDescription
typestringYes
settingsobjectYes
jobNamestringNo (default: "estimate")
atomCountintegerNo (default: null)
ParameterTypeRequiredDescription
modalitystringNo (default: null)
functionstringNo (default: null)
categorystringNo (default: null)
tagstringNo (default: null)
searchstringNo (default: null)
custombooleanNo (default: null)

No parameters.

ParameterTypeRequiredDescription
typesstringNo (default: null)
searchstringNo (default: null)
limitintegerNo (default: 100)
offsetintegerNo (default: 0)
includeMetadatabooleanNo (default: false)
ParameterTypeRequiredDescription
limitintegerNoMaximum number of folders to return (default: 20)
offsetintegerNoNumber of folders to skip (default: 0)
loadAllenumNoLoad all folders without pagination - one of: true
ParameterTypeRequiredDescription
jobNamestringYes
fileNamestringYes
maxSizeMBintegerNo (default: 10)
ParameterTypeRequiredDescription
jobNamestringYes
maxLinesintegerNo (default: 500)
ParameterTypeRequiredDescription
jobTypestringYes
ParameterTypeRequiredDescription
jobNamestringNo (default: null)
batchstringNo (default: null)
startKeystringNo (default: null)
limitintegerNo (default: 1000)
organizationbooleanNo (default: null)
includeSubjobsbooleanNo (default: null)
jobEmailstringNo (default: null)
includeSequencesbooleanNo (default: false)
ParameterTypeRequiredDescription
runIdstringYes
ParameterTypeRequiredDescription
runIdstringYes
nodestringNo (default: null)
limitintegerNo (default: 25)
cursorstringNo (default: null)

No parameters.

ParameterTypeRequiredDescription
templateIdstringYes
versionstringNo (default: null)
ParameterTypeRequiredDescription
jobNamestringYesName of the job to get results for
jobEmailstringNoEmail of another member of your team (optional)
fileNamestringNoPath to a specific file in the job results (optional)
pdbsOnlybooleanNoReturn only PDB files (optional)
ParameterTypeRequiredDescription
jobNamestringYes

No parameters.

ParameterTypeRequiredDescription
statusstringNo (default: null)
templateIdstringNo (default: null)
ownerstringNo (default: null)
limitintegerNo (default: 50)
cursorstringNo (default: null)
ParameterTypeRequiredDescription
searchstringNo (default: null)
ownerstringNo (default: null)
isPublishedbooleanNo (default: null)
limitintegerNo (default: 50)
cursorstringNo (default: null)

No parameters.

ParameterTypeRequiredDescription
jobNamestringYes
typestringYes
settingsobjectYes
ParameterTypeRequiredDescription
namestringYes
bindingsobjectYes
pipelineobjectNo (default: null)
templateIdstringNo (default: null)
versionstringNo (default: null)
settingsobjectNo (default: null)
Write - Create new jobs, batches, or files.
ParameterTypeRequiredDescription
batchNamestringYes
typestringYes
settingsarrayNo (default: null)
jobNamesarrayNo (default: null)
fromJobstringNo (default: null)
fromFilestringNo (default: null)
sequenceFieldstringNo (default: "sequence")
topNintegerNo (default: null)
sharedSettingsobjectNo (default: null)
maxRuntimeSecondsintegerNo (default: null)
weightedHoursBudgetnumberNo (default: null)
ParameterTypeRequiredDescription
jobNamestringYesUnique name for the job
typestringYesTool to use for the job. IMPORTANT: Use getAvailableTools() to discover available tools dynamically. Tool list is updated frequently - do not rely on hardcoded values. Example workflow: 1. Call getAvailableTools(search="alphafold") to find tools 2. Call getJobSchema(jobType="alphafold") to get parameter schema 3. Call submitJob with the tool name and settings
settingsobjectYesJob-specific settings. Structure depends on job type. IMPORTANT: Use the getJobSchema tool to get the exact parameter schema for your job type. Example: getJobSchema(jobType="proteinmpnn") returns the detailed schema with all parameters. Documentation: https://app.tamarind.bio/api-docs
ParameterTypeRequiredDescription
namestringYes
bindingsobjectYes
pipelineobjectNo (default: null)
templateIdstringNo (default: null)
versionstringNo (default: null)
settingsobjectNo (default: null)
runNamestringNo (default: null)
projectstringNo (default: null)
idempotencyKeystringNo (default: null)
Destructive - Delete, cancel, or overwrite existing data.
ParameterTypeRequiredDescription
batchNamestringYesBatch or pipeline name — same value used as `batchName` for submit-batch or `pipeline_name` for buildPipeline.
ParameterTypeRequiredDescription
jobNamestringNoName of the job to cancel (preferred input).
jobIdstringNoDDB row Id (alternative input, use if already known).
ParameterTypeRequiredDescription
filePathstringNo (default: null)
folderstringNo (default: null)
ParameterTypeRequiredDescription
jobNamestringYes
ParameterTypeRequiredDescription
runIdstringYes
ParameterTypeRequiredDescription
filenamestringYes
contentstringNo (default: "")
encodingstringNo (default: "text")
contentTypestringNo (default: "application/octet-stream")

Each tool corresponds to the REST API endpoints documented in our API reference. Use the sidebar to explore each endpoint in detail.

Troubleshooting

Connector not appearing

  • Save configuration file in the correct location and restart your client
  • Verify JSON syntax is correct (no missing commas or brackets)

Authentication failing

  • Verify your credentials (OAuth client ID/secret or API key) are correct and active
  • For API key: ensure the key is passed via the x-api-key header
  • For OAuth: log in with your Tamarind account and try again if a timeout occurs

Changes not applying

  • Save the file, then completely quit and restart your client (not just refresh)

Tools not working

  • Verify your authentication is still valid and try reconnecting

Sandboxed clients (Claude.ai, Claude Desktop) block outbound network by default. The MCP connection still works - it rides the client's connector - but the assistant's own requests to mcp.tamarind.bio are blocked, which shows up as a 403 or a file upload that fails with "network unreachable" / HTTP 000. It is not an authentication failure (those return 401). Allow the domain's egress:

  • Claude Desktop / Claude.ai: Settings → Capabilities → enable Allow network egress → under Additional allowed domains add mcp.tamarind.bio, then retry.
  • Small files (≤ 4 MB) can be uploaded inline by the assistant without enabling egress.

Need help? Contact us at info@tamarind.bio