Base URL

https://alphasync.stjude.org/api/v1/

Authentication

The API does not require authentication. It is open for public use.

Endpoints

1. Residue Data

Get residue data for a protein

Retrieves data for all residues of a specific protein, including solvent-accessible surface area, core/surface categorization, structured/disordered categorization, secondary structure, proline isomerization states and dihedral angles.

GET /api/v1/protein/{acc}

• {acc}: The protein accession (e.g. UniProt accession "P31946")

Response: Returns an array of objects containing data for all residues of the specified protein.

2. Contact Data

Get all contacts for a protein

Retrieves all residue–residue contact data for a specific protein.

GET /api/v1/contacts/{acc}

• {acc}: The protein accession (e.g. UniProt accession "P31946")

Response: Returns an array of objects containing all contact data for the specified protein.

3. ID Mapping

Get mapping data

Exposes AlphaSync's internal mapping functionality, which uses perfect sequence matching between a specified version of UniProt or Ensembl and the identifier used in the AlphaFold Protein Structure Database (or, where none available, AlphaSync's own structure predictions).

Available database version: UniProt 2026_01 (latest).

GET /api/v1/map/{type}/{version}/{acc}

• {type}: The database type (i.e. "uniprot")
• {version}: The database version (i.e. "2026_01" for UniProt)
• {acc}: The protein identifier to be mapped to AlphaSync (e.g. UniProt accession "P31946")

Response: Returns an array of objects containing mapping data.

4. Sequence Mapping

Map protein sequence

Map a given protein sequence to identifiers in AlphaSync, using perfect sequence matching.

GET /api/v1/mapseq/{seq}

• {seq}: The protein sequence (e.g. "MTMDKSELV…")

Response: Returns an array of objects containing mapping data for the given sequence.

5. Structure Download

Get download URLs for a protein

Returns download URLs for protein .cif, .pae and parameter files for both AlphaSync and AlphaFold DB proteins.

Note: For proteins larger than 2700 aa (e.g. A2VEC9), multiple URLs will be returned (one per fragment).

GET /api/v1/structure/{acc}

• {acc}: The protein accession (e.g. UniProt accession "P31946")

Response: Returns an array of objects containing basic annotation, sequence and lists of download URLs for the specified protein.

Response Format

All responses are in JSON format. Successful requests will return an HTTP status code of 200 and the requested data. In case of errors, appropriate HTTP status codes (e.g. 400 for bad requests, 404 for not found) will be returned along with an error message in JSON format.

Error Responses

Error responses will have the following format:

{
  "error": "Error message description"
}

Common error responses include:

• 400 Bad Request: When required parameters are missing or invalid
• 404 Not Found: When the requested data is not available

Examples

The following examples use curl to demonstrate how to interact with the API. You can run these commands in your terminal to test the API directly.

Example 1: Get residue data

Request:

curl -H "Accept: application/json" -X GET "https://alphasync.stjude.org/api/v1/protein/P31946"

Response:

[
    {
        "aa": "M",
        "acc": "P31946",
        "afdb": "1",
        "asa": 243,
        "asa10": 92.2727,
        "chi1": -80.4096,
        "chi2": 172.501,
        "chi3": 163.943,
        "chi4": null,
        "chi5": null,
        "dis": "*",
        "dis10": ".",
        "iso": "",
        "omega": null,
        "phi": null,
        "plddt": 52.34,
        "plddt10": 88.9691,
        "psi": 122.602,
        "relasa": 1.19704,
        "relasa10": 0.480261,
        "sec": "",
        "site": 1,
        "surf": "S",
        "surf10": "S",
        "tau": 106.707
    },
    // ... more residues
]

Example 2: Get contact data

Request:

curl -H "Accept: application/json" -X GET "https://alphasync.stjude.org/api/v1/contacts/P31946"

Response:

[
    {
        "aa1": "M",
        "aa2": "E",
        "acc": "P31946",
        "afdb": "1",
        "atom1": "CA",
        "atom2": "OE2",
        "dist": 3.01522,
        "pae": 5,
        "site1": 3,
        "site2": 7,
        "type": "WeakPolarHBondContacts"
    },
    // ... more contacts
]

Example 3: Get mapping data

Request:

curl -H "Accept: application/json" -X GET "https://alphasync.stjude.org/api/v1/map/uniprot/2026_01/P31946"

Response:

[
    {
        "type": "uniprot",
        "version": "2026_01",
        "value": "P31946",
        "best": 1,
        "afdb": 1,
        "map": "P31946",
        "species": "HUMAN",
        "tax": 9606,
        "avg_plddt": 93.4736
    }
]

Example 4: Map protein sequence

Request:

curl -H "Accept: application/json" -X GET "https://alphasync.stjude.org/api/v1/mapseq/MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN"

Response:

[
    {
      "acc": "P31946",
      "name": "1433B_HUMAN",
      "species": "HUMAN",
      "tax": 9606,
      "frags": 1,
      "afdb": 1,
      "seq": "MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN"
    }
]

Example 5: Get structure download URLs

Request:

curl -H "Accept: application/json" -X GET "https://alphasync.stjude.org/api/v1/structure/P31946"

Response:

[
    {
        "acc": "P31946",
        "afdb": 1,
        "frags": 1,
        "name": "1433B_HUMAN",
        "seq": "MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN",
        "species": "HUMAN",
        "tax": 9606,
        "url_cif": ["https:\/\/alphafold.ebi.ac.uk\/files\/AF-P31946-F1-model_v4.cif"],
        "url_pae": ["https:\/\/alphafold.ebi.ac.uk\/files\/AF-P31946-F1-predicted_aligned_error_v4.json"]
    }
]

About

To learn more about the data AlphaSync provides, please have a look at the About section.

Contact

If you have any ideas or questions regarding the API, please contact Benjamin Lang via email. Thank you!