Query Zinc Binding Site Structures
ZincBind MCP Server: Access ZincBindDB's GraphQL API to query zinc binding site structures and protein data.
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
Execute GraphQL queries against the ZincBindDB API to access zinc binding site structures and protein data
Overview
ZincBind MCP Server
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. 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.
What it does
As a researcher or developer, I want to easily query and analyze zinc binding site data so that I can advance my understanding of protein structures and functions.
Big Job: Understand and analyze complex protein structures and their interactions.
Small Job: Retrieve specific zinc binding site information, PDB records, and coordination patterns from a comprehensive database.
Installation from source:
git clone <this-repository>
cd zincbind-mcp-server
npm install
npm run dev
Cloudflare Workers deployment:
wrangler auth login
npm run deploy
Example MCP configuration:
{
"mcpServers": {
"zincbind": {
"command": "npx",
"args": [
"mcp-remote",
"https://zincbind-mcp-server.quentincody.workers.dev/sse"
]
}
}
}
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.
FAQ
Common questions
Discussion
Questions & comments · 0
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