Alphafold Sovereign MCP

Answering a structural-biology or variant question usually means querying many public databases by hand - AlphaFold DB, Open Targets, ClinVar, gnomAD, and more - and reconciling their formats. This server wraps those sources behind one set of MCP tool calls that run as a local process on your own machine, with no hosted service of ours in the path, no telemetry, and a local SQLite knowledge graph that never leaves…. Its 30 documented tools cover disease, variant, phenotype, target.

People connecting memory tools to Claude, Cursor, VS Code, or another MCP client. The project is written in Python.

VERIFIED ACTIVE

LAST COMMIT 2026-08-24 · ★ 4 · #82 OF 259 MAINTAINED MEMORY · VERIFIED 2026-08-25

Apache-2.0 · Python servers · how we verify → /methodology

01 · Install Alphafold Sovereign MCP

before you install - you'll need

Set ALPHAFOLD_OFFLINE before connecting.

Claude Code

claude mcp add smaniches-alphafold-sovereign-mcp -- uvx alphafold-sovereign-mcp

Claude Desktop / Cursor / VS Code - add to config

{
  "mcpServers": {
    "smaniches-alphafold-sovereign-mcp": {
      "command": "uvx",
      "args": [
        "alphafold-sovereign-mcp"
      ]
    }
  }
}

Same JSON for Cursor. For VS Code, rename the top-level key from `mcpServers` to `servers`.

Using another client? Same JSON, different key

Claude Desktop · mcpServers

Cursor · mcpServers

VS Code · servers

Windsurf · mcpServers

Zed · context_servers

Cline · mcpServers

Roo Code · mcpServers

Continue · mcpServers

LibreChat · mcpServers

Gemini CLI · mcpServers

Codex CLI · mcp_servers

Full setup guides: every client.

02 · Evidence

Security posture

What to check before giving this server access to your agent - from the registry, GitHub, and our own probes. We don't score safety; we show what's verifiable.

runs as local process (stdio) - runs on your machine with your user's permissions

license Apache-2.0 - declared in the repository

pypi package alphafold-sovereign-mcp - check the name against the project README before installing (PyPI has no namespace ownership)

registry namespace io.github.smaniches is GitHub-verified and matches the repo owner

03 · What Alphafold Sovereign MCP can do

Prose above is summarized from the project's README and registry record - no invented capabilities.

What you can build

With this server connected, an agent can retrieve an AlphaFold model: metadata, download URLs, optional coordinates, search locally stored variant triage results, search locally stored protein assessments, and export tables to JSON for pandas/ML pipelines.

Capability map

Tools grouped from the project's README - what Alphafold Sovereign MCP lets an agent do.

Disease

6 tools - e.g. MONDO record + hierarchy + ICD cross-references; Top drug targets for a MONDO disease (Open Targets); Parallel profiling across curated MONDO diseases

lookup_disease · get_disease_targets · get_common_disease_targets · get_orphan_disease_atlas · compare_disease_target_overlap · map_disease_drug_landscape

read & search

5 tools - e.g. Full-text MONDO ontology search; Top diseases for a UniProt target (Open Targets); Cross-species structural divergence (TDA + Ensembl orthologs)

search_diseases · get_target_diseases · find_evolutionary_structural_shifts · query_variant_database · get_knowledge_graph_stats

Phenotype

3 tools - e.g. HPO term + associated diseases; HPO phenotypes + gnomAD constraint for a gene; HPO → diseases → OT targets → UniProt IDs

lookup_phenotype · get_gene_phenotype_profile · phenotype_to_structures

Protein

3 tools - e.g. UniProt → multi-source briefing; Retrieve an AlphaFold model: metadata, download URLs, optional coordinates; Search locally stored protein assessments

synthesize_protein_dossier · get_protein_structure · query_protein_database

Drug

2 tools - e.g. MONDO → candidates ranked by OT evidence × ChEMBL phase; Traverse the local drug–gene–disease graph

find_drug_repurposing_candidates · find_drug_gene_network

Triage

1 tool - e.g. HGVS → ClinVar + gnomAD constraint (disease/structure context: pointer notes)

triage_variant_3d

Resolve

1 tool - e.g. ICD-10 code → MONDO disease record

resolve_icd10_to_mondo

Generate

1 tool - e.g. HGVS → multi-source report + draft ACMG/AMP criteria

generate_variant_clinical_report

Latest releases

v1.4.7 · 2026-08-20

1.4.7 (2026-08-20) · close exact-head gate failures · run image as non-root · verify published artifact bytes and Sigstore bundles · close published-release verifier trust gaps · harden container runtime and release…

v1.4.6 · 2026-08-20

1.4.6 (2026-08-20) · constrain upstream requests to configured origin

v1.4.5 · 2026-08-10

1.4.5 (2026-08-10) · make artifact toolchain deterministic and bind SBOM to wheel

04 · Who maintains Alphafold Sovereign MCP

alphafold-sovereign-mcp is maintained by smaniches. We track 3 MCP servers from smaniches - 3 actively maintained, 21 combined GitHub stars, oldest repo from Nov 2025. Full record: all servers from smaniches.

05 · Facts

repository: github.com/smaniches/alphafold-sovereign-mcp
category: memory - ranked #82 of 259 actively-maintained memory servers as of 2026-08-25.
release cadence: 10+ releases in the last 90 days (latest 2026-08-20)
registry: io.github.smaniches/alphafold-sovereign-mcp (active, first published 2026-06-09 · 10 versions)
packages: pypi:alphafold-sovereign-mcp

06 · Alphafold Sovereign MCP FAQ

Is Alphafold Sovereign MCP still maintained?

Yes - as of 2026-08-25, its last commit was 2026-08-24 and it shipped 10+ releases in the last 90 days. We re-verify nightly.

What can Alphafold Sovereign MCP do?

How do I install Alphafold Sovereign MCP?

Run `uvx alphafold-sovereign-mcp`. The README documents one environment variable (ALPHAFOLD_OFFLINE) to set first. Set ALPHAFOLD_OFFLINE before connecting. You can also paste the ready-made client config above.

Does Alphafold Sovereign MCP run locally?

Yes - it's a stdio server: it runs on your machine (via uvx) with your user's permissions. Your data stays local unless the server itself calls external APIs.

07 · Alternatives to Alphafold Sovereign MCP

Alternatives to Alphafold Sovereign MCP

Maintained memory servers if Alphafold Sovereign MCP isn't the fit.

Pairs well with

Servers that cover what Alphafold Sovereign MCP doesn't - only shown when the pairing reason fits the companion.

More memory MCP servers · Rmbr · Memex (stifler7) · Adam Framework · Local Memory

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