ChEMBL-MCP-Server

by BioMCP-Hub

325 downloads Not rated yet

GitHub

About

# ChEMBL-MCP-Server A FastMCP wrapper server based on the chembl_webresource_client package, providing API access to the ChEMBL database. ## Features - Complete API access to the ChEMBL database - Asynchronous API calls implemented using FastMCP framework - Built-in error handling and timeout mechanisms - Support for…

Explore

- Complete API access to the ChEMBL database
- Asynchronous API calls implemented using FastMCP framework
- Built-in error handling and timeout mechanisms
- Support for both HTTP and stdio transport methods
- Complete type annotations and docstrings

Setting up with Highlight

This MCP is not yet compatible with Highlight’s one-click setup. However, you can still use it with Highlight by following these steps:

Download and install Highlight from highlightai.com/download
Navigate to the plugins tab and select "Add Custom Plugin"
Configure the plugin with the settings below

Plugin Name ChEMBL-MCP-Server

Command (node, npx, python, etc.)

Please refer to the README for specific instructions on how to obtain API keys or other required environment variables.
Enable "Start Automatically" if you want the plugin to start when Highlight launches

Setting up with Cursor

Open Cursor's settings
Navigate to the MCP section
Click "Add new Global MCP server"
Copy and paste the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "chembl-mcp-server": {
            "chembl-mcp-server-biomcp-hub": {
                "command": "python",
                "args": [
                    "chembl_searver.py"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "chembl-mcp-server": {
            "chembl-mcp-server-biomcp-hub": {
                "command": "python",
                "args": [
                    "chembl_searver.py"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "chembl-mcp-server": {
            "chembl-mcp-server-biomcp-hub": {
                "command": "python",
                "args": [
                    "chembl_searver.py"
                ]
            }
        }
    }
}

Setting up with Claude Desktop

Open Claude Desktop's settings
Go to the Integrations tab
Click "Add MCP Server"
Use the configuration below based on your operating system

Note: Make sure Claude Desktop is running before attempting to connect.

JSON

{
    "mcpServers": {
        "chembl-mcp-server": {
            "chembl-mcp-server-biomcp-hub": {
                "command": "python",
                "args": [
                    "chembl_searver.py"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "chembl-mcp-server": {
            "chembl-mcp-server-biomcp-hub": {
                "command": "python",
                "args": [
                    "chembl_searver.py"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "chembl-mcp-server": {
            "chembl-mcp-server-biomcp-hub": {
                "command": "python",
                "args": [
                    "chembl_searver.py"
                ]
            }
        }
    }
}

Setting up with Windsurf

Open Windsurf's preferences
Go to the Integrations section
Click "Add MCP Integration"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "chembl-mcp-server": {
            "chembl-mcp-server-biomcp-hub": {
                "command": "python",
                "args": [
                    "chembl_searver.py"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "chembl-mcp-server": {
            "chembl-mcp-server-biomcp-hub": {
                "command": "python",
                "args": [
                    "chembl_searver.py"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "chembl-mcp-server": {
            "chembl-mcp-server-biomcp-hub": {
                "command": "python",
                "args": [
                    "chembl_searver.py"
                ]
            }
        }
    }
}

Setting up with Cline

Open Cline's settings
Navigate to the Integrations section
Click "Add MCP Server"
Copy and paste the configuration below based on your operating system

Note: Make sure to restart Cline after adding the configuration.

JSON

{
    "mcpServers": {
        "chembl-mcp-server": {
            "chembl-mcp-server-biomcp-hub": {
                "command": "python",
                "args": [
                    "chembl_searver.py"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "chembl-mcp-server": {
            "chembl-mcp-server-biomcp-hub": {
                "command": "python",
                "args": [
                    "chembl_searver.py"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "chembl-mcp-server": {
            "chembl-mcp-server-biomcp-hub": {
                "command": "python",
                "args": [
                    "chembl_searver.py"
                ]
            }
        }
    }
}

Setting up with Goose

Open Goose's preferences
Go to the Integrations tab
Select "MCP Servers"
Click "Add New Server"
Use the configuration below based on your operating system

JSON

{
    "mcpServers": {
        "chembl-mcp-server": {
            "chembl-mcp-server-biomcp-hub": {
                "command": "python",
                "args": [
                    "chembl_searver.py"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "chembl-mcp-server": {
            "chembl-mcp-server-biomcp-hub": {
                "command": "python",
                "args": [
                    "chembl_searver.py"
                ]
            }
        }
    }
}

JSON

{
    "mcpServers": {
        "chembl-mcp-server": {
            "chembl-mcp-server-biomcp-hub": {
                "command": "python",
                "args": [
                    "chembl_searver.py"
                ]
            }
        }
    }
}

From the repository

Clone the repository, install dependencies with pip install -r requirements.txt, then start the server using python chembl_searver.py. Configure it via command-line parameters such as --host, --port, --transport (http or stdio), and --log-level.

`example_canonicalizeSmiles`

Canonicalize SMILES strings

`example_smiles2inchi`

Convert SMILES to InChI

`example_smiles2svg`

Convert SMILES to SVG image

`example_structuralAlerts`

Get structural alerts

- example_canonicalizeSmiles: Canonicalize SMILES strings
- example_smiles2inchi: Convert SMILES to InChI
- example_smiles2svg: Convert SMILES to SVG image
- example_structuralAlerts: Get structural alerts
- More chemical tool APIs...

Claude Desktop / Cursor

Paste into your MCP client config file to install this server.

{
    "mcpServers": {
        "chembl-mcp-server": {
            "chembl-mcp-server-biomcp-hub": {
                "command": "python",
                "args": [
                    "chembl_searver.py"
                ]
            }
        }
    }
}

McpServers

{
    "chembl-mcp-server-biomcp-hub": {
        "command": "python",
        "args": [
            "chembl_searver.py"
        ]
    }
}

A FastMCP wrapper server based on the chembl_webresource_client package, providing API access to the ChEMBL database.

Features

Installation

```bash

No reviews yet — be the first

Use Google, GitHub, or an email account so ratings stay tied to real people.

Email sign in

No reviews posted yet.

About

Explore

Setting up with Highlight

From the repository

example_canonicalizeSmiles

example_smiles2inchi

example_smiles2svg

example_structuralAlerts

Claude Desktop / Cursor

McpServers

Features

Installation

More like this

Sequential Thinking

Redis

Filesystem

EverArt

`example_canonicalizeSmiles`

`example_smiles2inchi`

`example_smiles2svg`

`example_structuralAlerts`