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Bio-Agents MCP Server

@dogeplusplus

Repository

Basic information

Category

Other

Transports

stdio

Author

dogeplusplus

About Bio-Agents MCP Server

MCP servers for Protein Data Bank, ChemBL, and other life science data (WIP), with Ollama client for local testing.

#biology#protein-data-bank#agents#chembl-web-client#ollama#model-context-protocol#mcp-server

Bio-Agents MCP Server config

Add this server to your MCP-compatible client using the configuration below.

{
  "mcpServers": {
    "bio-agents-mcp": {
      "command": "docker",
      "args": [
        "build",
        "-t",
        "<module-name>",
        "."
      ]
    }
  }
}

Bio-Agents MCP Server tools

Tool list not available yet

This listing does not currently have a tool list to display. This does not mean the server has no tools; check its documentation for supported capabilities.

We auto-extract tools from the README. The maintainer can list them under a ## Tools heading to populate this section.

Overview

What is Bio-Agents MCP?

Bio-Agents MCP is a collection of microservices and clients for natural language interaction with biological databases, including the Protein Data Bank (PDB) and ChEMBL chemical database, built using the FastMCP framework.

How to use Bio-Agents MCP?

Copy the example environment file, build Docker images with make build, start all services with make up, then launch the web interface with make run-chainlit and visit http://localhost:8000 to query biological data.

Key features of Bio-Agents MCP

  • LLM client with web UI (Chainlit) and terminal modes
  • PDB MCP Server for Protein Data Bank API
  • ChEMBL MCP Server for chemical database API
  • Docker Compose to run all services together
  • Makefile for common tasks (build, up, down, restart)
  • Each module can run independently or together

Use cases of Bio-Agents MCP

  • Query protein structures and annotations from PDB using natural language
  • Search chemical compounds and bioactivity data via ChEMBL
  • Combine biological and chemical data through an LLM interface

Frequently asked questions

1

What components does it include?

It includes an LLM Client (web UI and terminal), PDB MCP Server, and ChEMBL MCP Server.

2

How do I start the system?

Configure environment with `cp .env.example .env`, then run `make build` and `make up`, followed by `make run-chainlit`.

3

What transport does it use?

The architecture uses FastMCP framework; services communicate via Docker networking (implied by Docker Compose).

4

What are the runtime requirements?

Docker and Docker Compose are required to run all services together. Each service has its own Dockerfile.

5

Where are configuration files located?

Configuration files are in the `conf/` directory. Detailed documentation for each service is in its own README.

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