PLMC MCP

Evolutionary coupling model training using PLMC via Docker

An MCP (Model Context Protocol) server for evolutionary coupling analysis with 2 core tools:

• Convert protein sequence alignments from A3M to A2M format
• Train PLMC evolutionary coupling models from sequence alignments

Quick Start with Docker

Approach 1: Pull Pre-built Image from GitHub

The fastest way to get started. A pre-built Docker image is automatically published to GitHub Container Registry on every release.

# Pull the latest image
docker pull ghcr.io/macromnex/plmc_mcp:latest

# Register with Claude Code (runs as current user to avoid permission issues)
claude mcp add plmc -- docker run -i --rm --user `id -u`:`id -g` -v `pwd`:`pwd` ghcr.io/macromnex/plmc_mcp:latest

Note: Run from your project directory. `pwd` expands to the current working directory.

Requirements:

• Docker
• Claude Code installed

That's it! The PLMC MCP server is now available in Claude Code.

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Approach 2: Build Docker Image Locally

Build the image yourself and install it into Claude Code. Useful for customization or offline environments.

# Clone the repository
git clone https://github.com/MacromNex/plmc_mcp.git
cd plmc_mcp

# Build the Docker image
docker build -t plmc_mcp:latest .

# Register with Claude Code (runs as current user to avoid permission issues)
claude mcp add plmc -- docker run -i --rm --user `id -u`:`id -g` -v `pwd`:`pwd` plmc_mcp:latest

Note: Run from your project directory. `pwd` expands to the current working directory.

Requirements:

• Docker
• Claude Code installed
• Git (to clone the repository)

About the Docker Flags:

• -i — Interactive mode for Claude Code
• --rm — Automatically remove container after exit
• --user `id -u`:`id -g` — Runs the container as your current user, so output files are owned by you (not root)
• -v — Mounts your project directory so the container can access your data

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Verify Installation

After adding the MCP server, you can verify it's working:

# List registered MCP servers
claude mcp list

# You should see 'plmc' in the output

In Claude Code, you can now use all 2 PLMC tools:

• plmc_convert_a3m_to_a2m
• plmc_generate_model

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Next Steps

• Detailed documentation: See detail.md for comprehensive guides on:
  • Available MCP tools and parameters
  • Local Python environment setup (alternative to Docker)
  • Example workflows and use cases
  • Troubleshooting

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Usage Examples

Once registered, you can use the PLMC tools directly in Claude Code. Here are some common workflows:

Example 1: Build an Evolutionary Coupling Model

I have created an A3M file for subtilisin BPN' at /path/to/subtilisin.a3m. Can you help build an EV model using the plmc MCP and create it in /path/to/plmc/ directory? The wild-type sequence is at /path/to/wt.fasta.

Example 2: Convert A3M to A2M Format

I have an A3M alignment file at /path/to/protein.a3m from MMseqs2. Can you convert it to A2M format and remove query gaps using plmc_convert_a3m_to_a2m, saving to /path/to/protein.a2m?

Example 3: Full EV Model Workflow

I have an MSA in A3M format at /path/to/protein.a3m and wild-type sequence at /path/to/wt.fasta.
1. First convert the A3M to A2M format using plmc_convert_a3m_to_a2m
2. Then train a PLMC model using plmc_generate_model, saving parameters to /path/to/plmc/

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Troubleshooting

Docker not found?

docker --version  # Install Docker if missing

Claude Code not found?

# Install Claude Code
npm install -g @anthropic-ai/claude-code

Model training failed?

• Ensure the A2M alignment file has the correct format (no query gaps)
• Verify the wild-type sequence matches the alignment focus sequence
• Check that the alignment has sufficient sequence diversity

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License

MIT — Based on PLMC by Debbie Marks Lab.