MCP Catalog

ProteinMCP includes 38 MCP servers: 24 local tool-MCPs developed in-house and 14 public community MCPs.

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Quick Reference

pmcp avail             # List all available MCPs
pmcp info <name>       # Show MCP details (tools, runtime, description)
pmcp install <name>    # Install and register an MCP
pmcp status            # Show installed/registered status for all MCPs

Runtime Types

Runtime	Install method	GPU	MCPs
Python	quick_setup.sh creates local env/ venv	No	msa_mcp, mmseqs2_mcp, interpro_mcp, alphafold2_mcp, alphafold3_mcp, …
Docker	docker build or docker pull	Yes	esm_mcp, prottrans_mcp, plmc_mcp, ev_onehot_mcp, bindcraft_mcp, boltzgen_mcp

Categories

Category	MCPs	Description
Structure Prediction	5	AlphaFold2/3, Boltz, Chai-1, ESMFold
Protein Design	4	ProteinMPNN, LigandMPNN, RFdiffusion2, Rosetta
Binder Design	2	BindCraft, BoltzGen
Molecular Dynamics	2	AMBER, GROMACS
Fitness Modeling	5	ESM, EV+OneHot, MutCompute, PLMC, ProtTrans
Sequence Analysis	3	MMseqs2, MSA, InterPro
Immunology	2	NetMHCpan, NetMHCIIpan
Other Tools	1	Protein-Sol
Public MCPs	14	Community-contributed servers

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Table of contents

• Structure Prediction
• Protein Design
• Binder Design
• Molecular Dynamics
• Fitness Modeling
• Sequence Analysis
• Immunology
• Other Tools
• Public MCPs