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zeinab-sheikhi

mcp-alphafold

by zeinab-sheikhi
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Python
Hybrid

Server Configuration

Describes the environment variables required to run the server.

NameRequiredDescriptionDefault

No arguments

Instructions

Guidance the server publishes about itself, which clients place ahead of the tool catalog so the model reads it before choosing anything.

This server publishes no instructions, or was last inspected before Glama recorded them.

Capabilities

Features and capabilities supported by this server

Protocol revision2025-11-25

CapabilityDetails
tools
{
  "listChanged": true
}
prompts
{
  "listChanged": false
}
resources
{
  "subscribe": false,
  "listChanged": false
}
experimental
{}

Tools

Functions exposed to the LLM to take actions

NameDescription
get_alphafold_predictionA

This tool retrieves all available AlphaFold models for a specified UniProt accession. It allows querying by the UniProt accession or by the CRC64 checksum of the UniProt sequence.

Arguments

  • qualifier (str): UniProt accession (e.g., 'Q5VSL9').

  • sequence_checksum (str, optional): CRC64 checksum of the UniProt sequence.

Example Input:

  • qualifier: Q5VSL9

  • sequence_checksum: 5F9BA1D4C7DE6925

Response Structure

The response will be a list of objects, each containing detailed information about the available AlphaFold models.

Example Output:

[
  {
    "entryId": "AF-Q5VSL9-F1",
    "gene": "STRIP1",
    "sequenceChecksum": "5F9BA1D4C7DE6925",
    "sequenceVersionDate": "2004-12-07",
    "uniprotAccession": "Q5VSL9",
    "uniprotId": "STRP1_HUMAN",
    "uniprotDescription": "Striatin-interacting protein 1",
    "taxId": 9606,
    "organismScientificName": "Homo sapiens",
    "uniprotStart": 1,
    "uniprotEnd": 837,
    "uniprotSequence": "MEPAVGGPGPLIVNNKQPQPPPPPPPAAAQPPPGAPRAAAGLLPGGKAREFN...",
    "modelCreatedDate": "2022-06-01",
    "latestVersion": 4,
    "allVersions": [1, 2, 3, 4],
    "bcifUrl": "https://alphafold.ebi.ac.uk/files/AF-Q5VSL9-F1-model_v4.bcif",
    "cifUrl": "https://alphafold.ebi.ac.uk/files/AF-Q5VSL9-F1-model_v4.cif",
    "pdbUrl": "https://alphafold.ebi.ac.uk/files/AF-Q5VSL9-F1-model_v4.pdb",
    "paeImageUrl": "https://alphafold.ebi.ac.uk/files/AF-Q5VSL9-F1-predicted_aligned_error_v4.png",
    "paeDocUrl": "https://alphafold.ebi.ac.uk/files/AF-Q5VSL9-F1-predicted_aligned_error_v4.json",
    "amAnnotationsUrl": "https://alphafold.ebi.ac.uk/files/AF-Q5VSL9-F1-aa-substitutions.csv",
    "amAnnotationsHg19Url": "https://alphafold.ebi.ac.uk/files/AF-Q5VSL9-F1-hg19.csv",
    "amAnnotationsHg38Url": "https://alphafold.ebi.ac.uk/files/AF-Q5VSL9-F1-hg38.csv",
    "isReviewed": true,
    "isReferenceProteome": true
  }
]
get_uniprot_summaryC

This tool fetches AlphaFold model predictions for a given UniProt residue range. The tool takes in a UniProt accession number (AC), entry name (ID), or CRC64 checksum and returns detailed information about the structure models available for the specified sequence range.

Arguments

  • qualifier (str): UniProtKB accession number (AC), entry name (ID), or CRC64 checksum of the UniProt sequence (e.g., 'Q5VSL9').

Example Input:

  • qualifier: Q5VSL9

Response Structure

The response includes detailed information about the UniProt entry and its associated AlphaFold models.

Example Response:

{
  "uniprot_entry": {
    "ac": "Q5VSL9",
    "id": "STRP1_HUMAN",
    "uniprot_checksum": "5F9BA1D4C7DE6925",
    "sequence_length": 837,
    "segment_start": 1,
    "segment_end": 837
  },
  "structures": [
    {
      "summary": {
        "model_identifier": "AF-Q5VSL9-F1",
        "model_category": "AB-INITIO",
        "model_url": "https://alphafold.ebi.ac.uk/files/AF-Q5VSL9-F1-model_v4.cif",
        "model_format": "MMCIF",
        "model_type": null,
        "model_page_url": "https://alphafold.ebi.ac.uk/entry/Q5VSL9",
        "provider": "AlphaFold DB",
        "number_of_conformers": null,
        "ensemble_sample_url": null,
        "ensemble_sample_format": null,
        "created": "2022-06-01",
        "sequence_identity": 1,
        "uniprot_start": 1,
        "uniprot_end": 837,
        "coverage": 1,
        "experimental_method": null,
        "resolution": null,
        "confidence_type": "pLDDT",
        "confidence_version": null,
        "confidence_avg_local_score": 80.82,
        "oligomeric_state": null,
        "preferred_assembly_id": null,
        "entities": [
          {
            "entity_type": "POLYMER",
            "entity_poly_type": "POLYPEPTIDE(L)",
            "identifier": "Q5VSL9",
            "identifier_category": "UNIPROT",
            "description": "Striatin-interacting protein 1",
            "chain_ids": [
              "A"
            ]
          }
        ]
      }
    }
  ]
}
get_annotationsB

This tool retrieves all annotations for a specified UniProt residue range. It allows querying by the UniProt accession and the annotation type (e.g., MUTAGEN for AlphaMissense).

Arguments

  • qualifier (str): UniProt accession (e.g., 'Q5VSL9').

  • annotation_type (str): Type of annotation (e.g., 'MUTAGEN' for AlphaMissense).

Example Input:

  • qualifier: Q5VSL9

  • annotation_type: MUTAGEN

Response Structure

The response includes detailed information about the UniProt entry and its associated annotations.

Example Output:

{
  "accession": "Q5VSL9",
  "id": "STRP1_HUMAN",
  "sequence": "MEPAVGGPGPLIVNNKQPQPPPPPPPAAAQPPPGAPRAAAGLLPGGKAREFNRNQRKDSEGYSESPDLEFEYADTDKWAAELSELYSYTEGPEFLMNRKCFEEDFRIHVTDKKWTELDTNQHRTHAMRLLDGLEVTAREKRLKVARAILYVAQGTFGECSSEAEVQSWMRYNIFLLLEVGTFNALVELLNMEIDNSAACSSAVRKPAISLADSTDLRVLLNIMYLIVETVHQECEGDKAEWRTMRQTFRAELGSPLYNNEPFAIMLFGMVTKFCSGHAPHFPMKKVLLLLWKTVLCTLGGFEELQSMKAEKRSILGLPPLPEDSIKVIRNMRAASPPASASDLIEQQQKRGRREHKALIKQDNLDAFNERDPYKADDSREEEEENDDDNSLEGETFPLERDEVMPPPLQHPQTDRLTCPKGLPWAPKVREKDIEMFLESSRSKFIGYTLGSDTNTVVGLPRPIHESIKTLKQHKYTSIAEVQAQMEEEYLRSPLSGGEEEVEQVPAETLYQGLLPSLPQYMIALLKILLAAAPTSKAKTDSINILADVLPEEMPTTVLQSMKLGVDVNRHKEVIVKAISAVLLLLLKHFKLNHVYQFEYMAQHLVFANCIPLILKFFNQNIMSYITAKNSISVLDYPHCVVHELPELTAESLEAGDSNQFCWRNLFSCINLLRILNKLTKWKHSRTMMLVVFKSAPILKRALKVKQAMMQLYVLKLLKVQTKYLGRQWRKSNMKTMSAIYQKVRHRLNDDWAYGNDLDARPWDFQAEECALRANIERFNARRYDRAHSNPDFLPVDNCLQSVLGQRVDLPEDFQMNYDLWLEREVFSKPISWEELLQ",
  "annotation": [
    {
      "type": "MUTAGEN",
      "description": "AM score",
      "source_name": "AFDB",
      "source_url": "https://alphafold.ebi.ac.uk/files/AF-Q5VSL9-F1-aa-substitutions.csv",
      "evidence": "COMPUTATIONAL/PREDICTED",
      "residues": [1, 2, 3, ...],
      "regions": [
        {
          "start": 1,
          "end": 837,
          "annotation_value": [0.3234, 0.3281, ...],
          "unit": null
        }
      ]
    }
  ]
}

Prompts

Interactive templates invoked by user choice

NameDescription

No prompts

Resources

Contextual data attached and managed by the client

NameDescription

No resources

Deploy Server
One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

TDQS

B3.4/5.0

Scored across 3 tools

Disambiguation2/5

get_alphafold_prediction and get_uniprot_summary both retrieve AlphaFold model information for a UniProt accession, with overlapping purposes. The descriptions do not clearly distinguish when to use one over the other, causing potential misselection. get_annotations is the only clearly distinct tool.

Naming Consistency5/5

All tool names follow a consistent get_<noun> pattern using snake_case. This predictable naming convention makes the tool set easy to navigate.

Tool Count5/5

With only 3 tools, the server is well-scoped and focused on AlphaFold data retrieval. Each tool has a meaningful role, even though two overlap functionally.

Completeness5/5

The server covers the core operations for AlphaFold: listing models, fetching a summary, and retrieving annotations. There are no obvious gaps for the intended domain, as structure URLs are included in responses.

Maintenance

ActivityInactive
ResponsivenessNo issues

Resources