gRNAde

Provides tools for RNA structure analysis, sequence evaluation, inverse design, and batch processing via the gRNAde framework.

python

0

GitHub Stars

python

Language

4 months ago

First Indexed

2 months ago

Catalog Refreshed

Documentation & install

Readme and setup notes from the catalogue, plus a client-ready config you can copy for your MCP host.

Installation

Add the following to your MCP client configuration file.

Configuration

View docs

{
  "mcpServers": {
    "macromnex-grnade_mcp": {
      "command": "python",
      "args": [
        "/absolute/path/to/grnade_mcp/src/server.py"
      ]
    }
  }
}

You set up and run the gRNAde MCP Server to analyze RNA structures, evaluate RNA sequences, inverse-design RNA sequences, and process batches. It provides a practical, scalable interface for researchers and developers to harness RNA design tools through an MCP client, enabling quick analyses and long-running workflows with job management.

How to use

You will interact with the MCP server through an MCP client. Register the server so the client can discover available tools, then run quick analyses or submit long-running design and batch jobs. Use the server for synchronous analyses that return results quickly and asynchronous tasks that provide you with a jobId to monitor progress.

How to install

Prerequisites ensure you can run the MCP server and its tooling.

pip install fastmcp loguru

How to install

Install with Claude Code CLI (Recommended) follow these steps to register the MCP server with Claude.

# Navigate to MCP directory
cd /path/to/grnade_mcp

# Register MCP server
claude mcp add geometric-rna-design -- python $(pwd)/src/server.py

# Verify installation
claude mcp list | grep geometric-rna-design
# Should show: geometric-rna-design: ... - ✓ Connected

# Start using
claude
# In Claude: "What tools are available from geometric-rna-design?"

Other installation methods

Alternative: Claude Desktop configuration can point Claude to the MCP server using a JSON config.

{
  "mcpServers": {
    "geometric-rna-design": {
      "command": "python",
      "args": ["/absolute/path/to/grnade_mcp/src/server.py"]
    }
  }
}

Alternative: Other MCP Clients

If you use a different MCP client, provide the Python path to the server script as shown.

{
  "mcpServers": {
    "geometric-rna-design": {
      "command": "python",
      "args": ["/absolute/path/to/src/server.py"],
      "env": {
        "PYTHONPATH": "/absolute/path/to/grnade_mcp"
      }
    }
  }
}

Available tools

analyze_rna_structure

Analyze RNA secondary structures and statistics, optionally using a provided sequence and producing an output file if requested.

evaluate_rna_sequences

Evaluate RNA sequences with computational metrics and optional basic statistics fallback when models are unavailable.

validate_rna_inputs

Validate RNA sequences and structures to ensure they meet expected formats before processing.

get_example_data

Provide example datasets and usage examples to help you get started quickly.

submit_rna_inverse_design

Submit RNA inverse design tasks to generate sequences that fold into specified structures or conform to a given pdb structure.

submit_batch_rna_pipeline

Submit a batch processing pipeline to handle multiple targets with evaluation and filtering steps.