Bio-Agents MCP

@dogeplusplus

关于 Bio-Agents MCP

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

基本信息

分类

其他

运行时

python

传输方式

stdio

发布者

dogeplusplus

配置

使用下面的配置,将此服务器添加到你的 MCP 客户端。

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

工具

未检测到工具

工具是从 README 中自动提取的。维护者可以在 ## Tools 标题下列出工具,即可填充这部分内容。

概览

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

FAQ from Bio-Agents MCP

What components does it include?

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

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.

What transport does it use?

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

What are the runtime requirements?

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

Where are configuration files located?

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

评论

其他分类下的更多 MCP 服务器

ICSS

不止于 CSS

Blender

Open-source MCP to use Blender with any LLM

Inbox Zero AI MCP

The world's best AI personal assistant for email. Open source app to help you reach inbox zero fast.

Sequential Thinking

modelcontextprotocol

Model Context Protocol Servers

Production-ready MCP integrations for AI applications

Klavis AI: MCP integration platforms that let AI agents use tools reliably at any scale