MCP

Query Zinc Binding Site Structures

Name: Query Zinc Binding Site Structures
Availability: OnlineOnly
Author: QuentinCody

ZincBind MCP Server: Access ZincBindDB's GraphQL API to query zinc binding site structures and protein data.

Connect

Works with cloudflare

QuentinCody

Maintainer?

Spark score

out of 100

Updated 4 months ago

Version 1.0.0

Models

claude

Add to Favorites

Why it matters

Access and query a comprehensive database of zinc binding site structures and protein data. Retrieve detailed information on PDB records, multimetallic sites, and liganding residues.

Outcomes

What it gets done

Query zinc binding sites from protein structures

Access PDB records with zinc coordination

Search for multimetallic sites and chain clusters

Explore liganding residues and binding geometries

Install

Add it to your toolbox

Run in your project directory:

curl -fsSL https://spark.entire.vc/get/vb-zincbind | bash

Capabilities

Tools your agent gets

zincbind_db_graphql_query

Execute GraphQL queries against the ZincBindDB API to access zinc binding site structures and protein data

Overview

ZincBind MCP Server

What it does

The ZincBind MCP Server acts as a connector to the ZincBindDB GraphQL API. It allows AI clients to query a comprehensive database for zinc binding site structures and associated protein data. Capabilities include accessing PDB records with zinc coordination, searching for multimetallic sites, and exploring liganding residues.

How it connects

Use this server when you need to programmatically access and analyze detailed information about zinc binding sites within protein structures. It is suitable for research, data analysis, and integration into AI workflows requiring specific biochemical and structural data.

Source README

An MCP server that provides access to the ZincBindDB GraphQL API for querying zinc binding site structures and protein data from a comprehensive zinc binding site database.

Installation

From Source Code

git clone <this-repository>
cd zincbind-mcp-server
npm install
npm run dev

Deploy to Cloudflare Workers

wrangler auth login
npm run deploy

Configuration

Claude Desktop

{
  "mcpServers": {
    "zincbind": {
      "command": "npx",
      "args": [
        "mcp-remote",
        "https://zincbind-mcp-server.quentincody.workers.dev/sse"
      ]
    }
  }
}

Available Tools

Tool	Description
`zincbind_db_graphql_query`	Execute GraphQL queries against the ZincBindDB API

Features

Query zinc binding sites from protein structures
Access to PDB (Protein Data Bank) records with zinc coordination
Search for multimetallic sites and chain clusters
Explore liganding residues and binding geometries
Schema introspection capabilities
Runs on Cloudflare Workers
GraphQL API access

Usage Examples

List zinc binding sites

Query specific PDB structure information

Perform schema introspection on the ZincBindDB

Find sites associated with specific protein structures

Explore zinc coordination patterns in proteins

Notes

Requires Node.js v18+, a Cloudflare account for deployment, and Wrangler CLI. Available under the MIT license with academic citation required for research use. The server runs at localhost:8787/sse for development and at the deployed URL for production.

Discussion