MHC Class II binding prediction using NetMHCIIpan-4.3 via Docker

An MCP (Model Context Protocol) server for MHC Class II peptide binding prediction and immunogenicity assessment with 18 tools:

• predict_peptide_binding -- Predict MHC II binding for peptides
• analyze_protein_sequence -- Map immunogenic epitope regions in proteins
• predict_custom_mhc_binding -- Binding prediction with custom alpha/beta chains
• predict_binding_affinity -- Multi-allele binding screening
• submit_peptide_prediction / submit_protein_analysis / submit_custom_mhc_prediction -- Async job submission
• submit_batch_multi_allele_screening / submit_large_peptide_screening / submit_multi_allele_screening -- Batch processing
• get_job_status / get_job_result / get_job_log / cancel_job / list_jobs -- Job management
• export_predictions_to_excel -- Export results to Excel format
• analyze_netmhcpan_output -- Parse raw NetMHCIIpan output
• get_server_info -- Server capabilities and supported alleles

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/netmhc2pan_mcp:latest

# Register with Claude Code (runs as current user to avoid permission issues)
claude mcp add netmhc2pan_mcp -- docker run -i --rm --user `id -u`:`id -g` -v `pwd`:`pwd` ghcr.io/macromnex/netmhc2pan_mcp:latest

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

Requirements:

• Docker
• Claude Code installed

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

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/netmhc2pan_mcp.git
cd netmhc2pan_mcp

# Build the Docker image
docker build -t netmhc2pan_mcp:latest .

# Register with Claude Code (runs as current user to avoid permission issues)
claude mcp add netmhc2pan_mcp -- docker run -i --rm --user `id -u`:`id -g` -v `pwd`:`pwd` netmhc2pan_mcp:latest

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
• -v -- Mounts your project directory

claude mcp list
# You should see 'netmhc2pan_mcp' in the output

In Claude Code, you can now use all 18 tools:

• predict_peptide_binding, analyze_protein_sequence, predict_custom_mhc_binding, predict_binding_affinity
• submit_peptide_prediction, submit_protein_analysis, submit_custom_mhc_prediction
• submit_batch_multi_allele_screening, submit_large_peptide_screening, submit_multi_allele_screening
• get_job_status, get_job_result, get_job_log, cancel_job, list_jobs
• export_predictions_to_excel, analyze_netmhcpan_output, get_server_info

• Detailed documentation: See detail.md for comprehensive guides including local installation, script usage, configuration files, demo data, allele lists, and troubleshooting

Use predict_peptide_binding with peptides "AAAGAEAGKATTE,AALAAAAGVPPADKY" for allele DRB1_0101 and include summary statistics

Run analyze_protein_sequence on @my_protein.fasta using allele DRB1_0101 with context-aware prediction enabled

Run predict_binding_affinity on @peptides.txt across alleles "DRB1_0101,DRB1_0301,DRB1_1501" and generate Excel output

Problem: Container not found or pull fails

# Verify Docker is running
docker info

# Pull with explicit tag
docker pull ghcr.io/macromnex/netmhc2pan_mcp:latest

Problem: Permission denied on output files

# Ensure you're using the --user flag
docker run -i --rm --user `id -u`:`id -g` -v `pwd`:`pwd` ghcr.io/macromnex/netmhc2pan_mcp:latest

Problem: MCP server not responding

# Re-register with Claude Code
claude mcp remove netmhc2pan_mcp
claude mcp add netmhc2pan_mcp -- docker run -i --rm --user `id -u`:`id -g` -v `pwd`:`pwd` ghcr.io/macromnex/netmhc2pan_mcp:latest

Problem: File paths not found inside container

# Make sure to run Claude Code from the directory containing your files
# The -v `pwd`:`pwd` flag mounts only the current directory
cd /path/to/your/project
claude

Problem: NetMHCIIpan binary errors inside container

# Test the container directly
docker run --rm ghcr.io/macromnex/netmhc2pan_mcp:latest --help

# If the binary fails, rebuild the image
docker build --no-cache -t netmhc2pan_mcp:latest .

Academic License -- Based on NetMHCIIpan-4.3 by DTU Bioinformatics. For commercial use, obtain a license from DTU Health Tech.

• NetMHCIIpan-4.3: Original software by DTU Bioinformatics
• MCP Integration: Built with FastMCP framework