AlphaFoldSAFE
A comprehensive Model Context Protocol (MCP) server that provides access to the AlphaFold Protein Structure Database through a rich set of tools and resources for protein structure prediction analysis.
Overview
From the repository's own README, as read at the audited commit. Badges and raw HTML are left out.
A comprehensive Model Context Protocol (MCP) server that provides access to the AlphaFold Protein Structure Database through a rich set of tools and resources for protein structure prediction analysis.
Overview
This MCP server enables seamless integration with AlphaFold's vast collection of protein structure predictions, offering tools for structure retrieval, confidence analysis, batch processing, and visualization preparation. Perfect for researchers, bioinformaticians, and structural biologists working with predicted protein structures.
Features
🧬 Core Structure Tools
- Structure Retrieval: Get AlphaFold predictions by UniProt ID
- Multi-format Downloads: Support for PDB, CIF, BCIF, and JSON formats
- Availability Checking: Verify if predictions exist for specific proteins
🔍 Search & Discovery
- Structure Search: Find proteins by name, gene, or organism
- Organism Browsing: List all available structures for specific species
- Coverage Statistics: Get comprehensive organism-level statistics
📊 Confidence & Quality Analysis
- Per-residue Confidence: Detailed confidence scores for each amino acid
- Region Analysis: Identify high/low confidence structural regions
- Quality Validation: Assess overall prediction reliability
⚡ Batch Processing
- Bulk Retrieval: Process multiple proteins simultaneously
- Batch Downloads: Efficient multi-structure downloads
- Parallel Analysis: Confidence analysis for protein sets
🔬 Comparative Analysis
- Structure Comparison: Side-by-side analysis of multiple proteins
- Similarity Search: Find structurally related proteins
- Coverage Comparison: Analyze prediction completeness
🎨 Visualization Integration
- PyMOL Scripts: Ready-to-use visualization scripts
- ChimeraX Integration: Confidence-colored structure viewing
- Custom Export Formats: F
72c00265efb6OBSERVED · 2026-10-08Connect
Built from this server's own package name, version and transport as found in its source — not copied from anyone's documentation, so it cannot drift against a page we do not control.
claude mcp add alphafold-server -- npx -y [email protected]
{
"mcpServers": {
"alphafold-server": {
"command": "npx",
"args": [
"-y",
"[email protected]"
]
}
}
}Exposed tools (19)
19 read · 0 write · 0 destructive.
| Tool | Risk | Description |
|---|---|---|
analyze_confidence_regions | read | Analyze confidence score distribution and identify high/low confidence regions |
batch_confidence_analysis | read | Analyze confidence scores for multiple proteins |
batch_download | read | Download multiple structure files |
batch_structure_info | read | Get structure information for multiple proteins simultaneously |
check_availability | read | Check if AlphaFold structure prediction is available for a UniProt ID |
compare_structures | read | Compare multiple AlphaFold structures for analysis |
download_structure | read | Download AlphaFold structure file in specified format |
export_for_chimerax | read | Export structure data formatted for ChimeraX visualization |
export_for_pymol | read | Export structure data formatted for PyMOL visualization |
find_similar_structures | read | Find AlphaFold structures similar to a given protein |
get_api_status | read | Check AlphaFold API status and database statistics |
get_confidence_scores | read | Get per-residue confidence scores for a structure prediction |
get_coverage_info | read | Get information about sequence coverage in the AlphaFold prediction |
get_organism_stats | read | Get statistics about AlphaFold coverage for an organism |
get_prediction_metadata | read | Get metadata about the prediction including version, date, and quality metrics |
get_structure | read | Get AlphaFold structure prediction for a specific UniProt ID |
list_by_organism | read | List all available structures for a specific organism |
search_structures | read | Search for available AlphaFold structures by protein name or gene |
validate_structure_quality | read | Validate and assess the overall quality of an AlphaFold prediction |
Trust audit
SAFEgrade B · trust 89/100 Nothing in the source contradicts what it says it does. Grade A is reserved for packages that have also passed the behavioural sandbox.
| Layer | What it checks | Result |
|---|---|---|
| L0 | Provenance & inventory | PASS |
| L1 | Static analysis of the code | PASS |
| L2 | Instruction surface (what it tells the agent) | PASS |
| L3 | Class-specific surface | PASS |
| L4 | Behavioural (sandbox) | SKIPPED |
What the source does
- Filesystem
- none-observed
- Network
- declared (5 observation(s))
- Shell
- none-observed
- Dependencies
- not all pinned
- Secrets in source
- none-found
Findings (1)
@modelcontextprotocol/sdk, axios, @types/node, typescript
Gates applied: no_behavioural_pass.
72c00265efb6full audit observations/trust-audit/mcp-server/augmented-nature__alphafold.json · Report an issue / request a re-scanAudit history
Every audit this server has had. A grade with a past is a grade somebody is still checking.
| Date | Source | Verdict | Grade | Score | Change |
|---|---|---|---|---|---|
| 2026-10-08 | 72c00265efb6 | SAFE | B | 89 | first audit |
Questions
What is the AlphaFold MCP server?
A comprehensive Model Context Protocol (MCP) server that provides access to the AlphaFold Protein Structure Database through a rich set of tools and resources for protein structure prediction analysis.
What tools does AlphaFold expose?
19 in total: 19 read-only, 0 that write, and 0 that can delete or overwrite. Every one is listed on this page with its risk.
Is AlphaFold safe to connect to an agent?
The audit found nothing in the source that contradicts what it says it does, and graded it B (89/100). Grade A is held back for packages that have also passed a sandboxed behavioural run, which is why a clean server reads B.
What credentials does AlphaFold need?
No credential environment variables were found in its source, so it appears to need none.
How does AlphaFold run?
It speaks stdio, so it runs as a local process your client starts. It is published on npm as alphafold-server at 1.0.0.
How current is this page?
The grade is for one exact copy of the source (72c00265efb6), read on 2026-10-08. The repository is watched and re-audited when it changes.