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JSON file format for AlphaFold Server jobs

You can download an example JSON file here; here we describe the contents of this example JSON file.

This JSON file consists of a list of dictionaries (even in the case of a single dictionary, a single-element list must be used), with each dictionary containing a job description. Therefore, you can specify multiple jobs in one JSON file.

Each job description contains a job name, a list of PRNG seeds (which can be an empty list for automated random seed assignment), and a list of entities (molecules) to be modeled.

AlphaFold Server JSON files are especially useful for automation of repetitive modeling jobs (e.g. to screen interactions of one protein with a small number of others). The easiest way to construct an initial JSON file is to run a modeling job via AlphaFold Server GUI and use it as a template. AlphaFold Server will produce a zip file containing modeling results. Inside the zip file you will find a JSON file named <job_name>_job_request.json containing the job inputs. These files offer a convenient starting point for generating new jobs as they are easily editable in standard text editors or in programming environments like Google Colab notebooks.

Note that comments are not allowed in JSON files.

Job name, seeds and sequences

  • name is a string with the job name. This is how the job will appear as in the job history table.
  • modelSeeds is a list of strings of uint32 seed values (e.g. ["1593933729", "4273"]). Seeds are used to run the modeling. We recommend providing an empty list, in which case a single random seed will be used. This is the recommended option.
  • sequences is a list of dictionaries that carry descriptions of the entities (molecules) for modeling.
{
  "name": "Test Fold Job Number One",
  "modelSeeds": [],
  "sequences": [...]
}

Entity types

Valid entity types mirror those available in the AlphaFold Server web interface:

  • proteinChain – used for proteins
  • dnaSequence – used for DNA (single strand)
  • rnaSequence – used for RNA (single strand)
  • ligand – used for allowed ligands
  • ion – used for allowed ions

Protein chains

sequence is a string containing protein sequence; the same limitations as in the UI are in place, e.g. only letters corresponding to amino acids are allowed, as defined by IUPAC. Only 20 standard amino acid type are supported.

count is the number of copies of this protein chain (integer).

glycans is an optional list of dictionaries that carries descriptions of the protein glycosylation.

  • residues is a string defining glycan. Please refer to the FAQ for the format description and allowed glycans.
  • position is a position of the amino acid to which the glycan is attached (integer, 1-based indexing).

modifications is an optional list of dictionaries that carries descriptions of the post-translational modifications.

  • ptmType is a string containing the CCD code of the modification; the same codes are allowed as in the UI.
  • position is a position of the modified amino acid (integer).
  • Allowed modifications: CCD_SEP, CCD_TPO, CCD_PTR, CCD_NEP, CCD_HIP, CCD_ALY, CCD_MLY, CCD_M3L, CCD_MLZ, CCD_2MR, CCD_AGM, CCD_MCS, CCD_HYP, CCD_HY3, CCD_LYZ, CCD_AHB, CCD_P1L, CCD_SNN, CCD_SNC, CCD_TRF, CCD_KCR, CCD_CIR, CCD_YHA
{
  "proteinChain": {
    "sequence": "PREACHINGS",

    "glycans": [
      {
        "residues": "NAG(NAG)(BMA)",
        "position": 8
      },
      {
        "residues": "BMA",
        "position": 10
      }
    ],

    "modifications": [
      {
        "ptmType": "CCD_HY3",
        "ptmPosition": 1
      },
      {
        "ptmType": "CCD_P1L",
        "ptmPosition": 5
      }
    ],

    "count": 1
  }
},
{
  "proteinChain": {
    "sequence": "REACHER",
    "count": 1
  }
}

DNA chains

Please note that the dnaSequence type refers to single stranded DNA. If you wish to model double stranded DNA, please add a second "dnaSequence", carrying the sequence of the reverse complement strand.

sequence is a string containing a DNA sequence; the same limitations as in the UI are in place, i.e. only letters A, T, G, C are allowed.

count is a number of copies of this DNA chain (integer).

modifications is an optional list of dictionaries that carries descriptions of the DNA chemical modifications.

  • modificationType is a string containing CCD code of modification; the same codes are allowed as in the UI.
  • basePosition is a position of the modified nucleotide (integer).
  • Allowed modifications: CCD_5CM, CCD_C34, CCD_5HC, CCD_6OG, CCD_6MA, CCD_1CC, CCD_8OG, CCD_5FC, CCD_3DR
{
  "dnaSequence": {
    "sequence": "GATTACA",

    "modifications": [
      {
        "modificationType": "CCD_6OG",
        "basePosition": 1
      },
      {
        "modificationType": "CCD_6MA",
        "basePosition": 2
      }
    ],

    "count": 1
  }
},
{
  "dnaSequence": {
    "sequence": "TGTAATC",
    "count": 1
  }
}

RNA chains

sequence is a string containing RNA sequence (single strand); the same limitations as in the UI are in place, e.g. only letters A, U, G, C are allowed.

count is a number of copies of this RNA chain (integer).

modifications is an optional list of dictionaries that carries descriptions of the RNA chemical modifications.

  • modificationType is a string containing CCD code of modification; the same codes are allowed as in the UI.
  • basePosition is a position of the modified nucleotide (integer).
  • Allowed modifications: CCD_PSU, CCD_5MC, CCD_OMC, CCD_4OC, CCD_5MU, CCD_OMU, CCD_UR3, CCD_A2M, CCD_MA6, CCD_6MZ, CCD_2MG, CCD_OMG, CCD_7MG, CCD_RSQ
{
  "rnaSequence": {
    "sequence": "GUAC",

    "modifications": [
      {
        "modificationType": "CCD_2MG",
        "basePosition": 1
      },
      {
        "modificationType": "CCD_5MC",
        "basePosition": 4
      }
    ],

    "count": 1
  }
}

Ligands

ligand is a string containing the CCD code of the ligand; the same codes are allowed as in the UI.

count is the number of copies of this ligand (integer).

Allowed ligands: CCD_ADP, CCD_ATP, CCD_AMP, CCD_GTP, CCD_GDP, CCD_FAD, CCD_NAD, CCD_NAP, CCD_NDP, CCD_HEM, CCD_HEC, CCD_PLM, CCD_OLA, CCD_MYR, CCD_CIT, CCD_CLA, CCD_CHL, CCD_BCL, CCD_BCB

{
  "ligand": {
    "ligand": "CCD_ATP",
    "count": 1
  }
},
{
  "ligand": {
    "ligand": "CCD_HEM",
    "count": 2
  }
}

Ions

ion is a string containing CCD code of the ion; the same codes are allowed as in the UI. The ion charge is implicitly specified by the CCD code.

count is a number of copies of this ion (integer).

Allowed ions: MG, ZN, CL, CA, NA, MN, K, FE, CU, CO

{
  "ion": {
    "ion": "MG",
    "count": 2
  }
},
{
  "ion": {
    "ion": "NA",
    "count": 3
  }
}

Additional modeling jobs

You may specify multiple jobs in one JSON file. This is an example of a simple job request for one protein chain and two copies of the palindromic DNA sequence:

{
  "name": "Test Fold Job Number Two",
  "modelSeeds": [],
  "sequences": [
    {
      "proteinChain": {
        "sequence": "TEACHINGS",
        "count": 1
      }
    },
    {
      "dnaSequence": {
        "sequence": "TAGCTA",
        "count": 2
      }
    }
  ]
}