Koskamo

Bindingdb MCP

The Bindingdb MCP server enables AI agents to query BindingDB for measured protein/small-molecule binding affinities. It offers tools to retrieve ligand affinities by UniProt target, identify protein targets by compound SMILES, and find affinities for ligands associated with PDB structures, linking potency data to PubMed citations.

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Package and access

Local package with source-attributed installation metadata. Koskamo does not execute packages during review.

Bindingdb MCP logo, by PipeworxCommunity listingLocal stdioSource reviewed; not executedPublished by Pipeworx
Vendor documentation

What you can do with it

  • Retrieve binding affinities for ligands against a specific UniProt target
  • Identify protein targets for a compound given its SMILES string
  • Find measured binding affinities for ligands associated with a PDB structure

Source and maintenance

Community listingRegistry 0.2.1MIT
mcp-registry: io.github.pipeworx-io/bindingdb@0.2.1Source repositoryProject website
Last repository push
Maintenance checked

Packages and installation

Source-provided package data. Koskamo has not executed or live-probed this package.

@pipeworx/mcp-bindingdb 0.2.1

npm
@pipeworx/mcp-bindingdb package definition
{
  "version": "0.2.1",
  "transport": "stdio",
  "identifier": "@pipeworx/mcp-bindingdb",
  "registryType": "npm",
  "environmentVariables": [
    {
      "name": "PIPEWORX_API_KEY",
      "description": "Optional Pipeworx API key. Without it calls are anonymous and capped daily; a free key raises the cap."
    }
  ]
}

Tools

Reported by the attributed source; not independently observed by Koskamo.

No tool definitions available.

Maintenance history

Public check and source-refresh events. Editorial and ownership records remain private.

  • · repository · passed · metadata changed · updated
  • · backfill · recorded · Pre-expansion baseline; unobserved rich metadata remains unknown

Connect from your client

Each snippet configures the same source-provided package; replace placeholders before use.

This server is operated by the named third party. Listing and endpoint checks are not an endorsement or a security audit. Review the operator's permissions, terms, and data handling before connecting. How listings are checked and corrected.

Cursor

Merge this local stdio configuration, replace every placeholder environment value, and restart Cursor. Koskamo has not executed this package.
Cursor configuration
{
  "mcpServers": {
    "bindingdb-mcp-pipeworx-mcp-bindingdb": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-bindingdb@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Cline

Merge this local stdio configuration, replace every placeholder environment value, and restart Cline. Koskamo has not executed this package.
Cline configuration
{
  "mcpServers": {
    "bindingdb-mcp-pipeworx-mcp-bindingdb": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-bindingdb@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

VS Code

Merge this local stdio configuration, replace every placeholder environment value, and restart VS Code. Koskamo has not executed this package.
VS Code configuration
{
  "servers": {
    "bindingdb-mcp-pipeworx-mcp-bindingdb": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-bindingdb@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

Claude Desktop

Merge this local stdio configuration, replace every placeholder environment value, and restart Claude Desktop. Koskamo has not executed this package.
Claude Desktop configuration
{
  "mcpServers": {
    "bindingdb-mcp-pipeworx-mcp-bindingdb": {
      "command": "npx",
      "args": [
        "-y",
        "@pipeworx/mcp-bindingdb@0.2.1"
      ],
      "env": {
        "PIPEWORX_API_KEY": "<YOUR_PIPEWORX_API_KEY>"
      }
    }
  }
}

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