{"$schema":"https://wellknown.network/schemas/agent-record-v1.json","schemaVersion":"1","id":"ag_j3mr6d3xnqx7","handle":"protein-design-mcp","url":"https://wellknown.network/agents/protein-design-mcp","links":{"self":"https://wellknown.network/agents/protein-design-mcp/record.json","html":"https://wellknown.network/agents/protein-design-mcp","markdown":"https://wellknown.network/agents/protein-design-mcp/record.md","api":"https://wellknown.network/api/v1/agents/protein-design-mcp","status":"https://wellknown.network/api/v1/agents/protein-design-mcp/status","claim":"https://wellknown.network/agents/protein-design-mcp/claim","claimApi":"https://wellknown.network/api/v1/claims","claimDescriptor":"https://wellknown.network/agents/protein-design-mcp/claim.json","badge":"https://wellknown.network/agents/protein-design-mcp/badge.svg","openapi":"https://wellknown.network/openapi.json","history":"https://wellknown.network/api/v1/agents/protein-design-mcp/history","tools":"https://wellknown.network/api/v1/agents/protein-design-mcp/tools"},"ard":{"identifier":"urn:air::server:protein-design-mcp","type":"application/mcp-server-card+json"},"kind":"mcp_server","declared":{"name":"protein-design-mcp","summary":"MCP server for protein design: RFdiffusion, ProteinMPNN, ESMFold, AlphaFold2, Boltz, PyRosetta, ESM2, OpenMM","description":"# Protein Design MCP Server\n\n[![PyPI](https://img.shields.io/pypi/v/protein-design-mcp)](https://pypi.org/project/protein-design-mcp/)\n[![Docker Hub](https://img.shields.io/docker/v/jeonghyeonkim8652/protein-design-mcp?label=docker%20hub&logo=docker)](https://hub.docker.com/r/jeonghyeonkim8652/protein-design-mcp)\n[![GHCR](https://img.shields.io/badge/ghcr.io-protein--design--mcp-blue?logo=github)](https://github.com/jasonkim8652/protein-design-mcp/pkgs/container/protein-design-mcp)\n[![Smithery](https://smithery.ai/badge/protein-design-mcp)](https://smithery.ai/server/protein-design-mcp)\n[![License](https://img.shields.io/badge/license-Apache%202.0-blue)](LICENSE)\n\nAn [MCP](https://modelcontextprotocol.io) server that gives LLM agents access to computational protein design tools. Ask your LLM to design binders, generate de novo folds, predict structures, score interfaces, or relax with Rosetta — it calls the right tool automatically.\n\n**19 tools total**, spanning generative design, structure prediction, physics-based scoring, and analysis. Built on RFdiffusion, ProteinMPNN, ESMFold, AlphaFold2, **Boltz-2**, **PyRosetta**, ESM2, and OpenMM.\n\n| Distribution | Tools out-of-the-box | Extras |\n|---|---|---|\n| `pip install \"protein-design-mcp[gpu]\"` | 13 core tools | `[rosetta]` (license required), `[boltz]` (isolated venv) |\n| `docker pull jeonghyeonkim8652/protein-design-mcp` | 13 core tools (GPU), 10 (CPU) | PyRosetta / Boltz not bundled (license + torch conflict) |\n\nThe 6 non-bundled tools (`rosetta_*` x4, `predict_*_boltz` x2) install cleanly via pip extras — see [Optional Tools](#optional-tools-pyrosetta--boltz-2).\n\n## Installation\n\nChoose the method that fits your situation. Listed from simplest to most customizable.\n\n---\n\n### 1. Auto-Setup (Recommended)\n\nOne command. Detects your environment, pulls Docker if available, writes MCP client config.\n\n```bash\npip install protein-design-mcp\nprotein-design-mcp-setup\n```\n\nWhat it does:\n- Checks for Docker and NVIDIA GPU\n- …","publisher":{"name":"Protein Design MCP Team","url":null},"homepage":"https://github.com/jasonkim8652/protein-design-mcp#readme","repository":"https://github.com/jasonkim8652/protein-design-mcp#readme","version":"1.0.0","license":"Apache-2.0","protocols":["mcp"],"tags":["mcp","protein-design","rfdiffusion","proteinmpnn","esmfold","alphafold2","boltz","pyrosetta","llm","ai"],"pricing":null,"endpoints":[{"url":"pypi:protein-design-mcp","type":"package_pypi","auth":null,"probeable":false}],"skills":null,"tools":null,"extra":null,"attribution":{"kind":"pypi","name":"pypi","license":"pypi","repoUrl":"pypi","summary":"pypi","version":"pypi","description":"pypi","homepageUrl":"pypi","publisherName":"pypi"}},"derived":{"capabilities":[{"slug":"media.3d","name":"3D & Design","confidence":1,"provenance":"derived"}],"categories":["media"],"language":"en"},"observed":{"status":"unknown","statusReason":"Distributed as a package to run locally; no network endpoint to check.","lastOkAt":null,"lastProbedAt":null,"statusComputedAt":null,"reliability30d":null,"latestObservations":[],"tools":null,"package":{"name":"protein-design-mcp","registry":"pypi","observedAt":"2026-11-03T22:25:40.994Z","publishedAt":"2026-04-15T04:24:08.379069Z","latestVersion":"1.0.0"},"toolSurface":null,"endpointFacts":[]},"verification":{"claimed":false,"claimedAt":null,"proofs":[]},"provenance":{"sources":[{"source":"pypi","key":"protein-design-mcp","url":"https://pypi.org/project/protein-design-mcp/","firstSeenAt":"2026-09-10T10:24:08.695Z","fetchedAt":"2026-11-03T22:24:35.791Z","normalizedAt":"2026-11-03T22:24:35.791Z"}]},"firstSeenAt":"2026-09-10T10:24:08.695Z","updatedAt":"2026-11-03T22:25:40.994Z"}