Input JSON Format

AlphaFast uses the standard AlphaFold 3 JSON input format. Place one or more .json files in your --input_dir.

Field Reference

Field	Type	Required	Description
`name`	string	Yes	Job name. Used for output directory naming.
`sequences`	array	Yes	Array of chain definitions (protein, ligand, etc.)
`modelSeeds`	array of int	Yes	Random seeds for inference. At least one seed required.
`dialect`	string	Yes	Must be `"alphafold3"`
`version`	int	Yes	Supported versions: `1`, `2`, `3`, or `4`

Optional Fields

Field	Type	Description
`bondedAtomPairs`	array	Custom bonded atom pair constraints
`userCCD`	string	Custom Chemical Component Dictionary (CCD) entries

Protein Chain

A single protein chain with chain ID "A":

{
  "name": "my_protein",
  "sequences": [
    {
      "protein": {
        "id": ["A"],
        "sequence": "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH"
      }
    }
  ],
  "modelSeeds": [42],
  "dialect": "alphafold3",
  "version": 1
}

Homomeric Complex

A homodimer where both chains A and B share the same sequence. List multiple chain IDs in the id array:

{
  "name": "my_homodimer",
  "sequences": [
    {
      "protein": {
        "id": ["A", "B"],
        "sequence": "GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGY"
      }
    }
  ],
  "modelSeeds": [1],
  "dialect": "alphafold3",
  "version": 1
}

Heteromeric Complex

Two different protein chains:

{
  "name": "my_heterodimer",
  "sequences": [
    {
      "protein": {
        "id": ["A"],
        "sequence": "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH"
      }
    },
    {
      "protein": {
        "id": ["B"],
        "sequence": "MHSSIVLATVLFVAIASASKTRELCMKSLEHAKVGTSKEAKQDGIDLYKHMFE"
      }
    }
  ],
  "modelSeeds": [1],
  "dialect": "alphafold3",
  "version": 1
}

Protein with Ligand

A protein chain with an ATP ligand, specified using its CCD code:

{
  "name": "protein_atp",
  "sequences": [
    {
      "protein": {
        "id": ["A"],
        "sequence": "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH"
      }
    },
    {
      "ligand": {
        "id": ["B"],
        "ccdCodes": ["ATP"]
      }
    }
  ],
  "modelSeeds": [1],
  "dialect": "alphafold3",
  "version": 1
}

Multiple Seeds

Provide multiple seeds to generate independent structure samples:

{
  "name": "multi_seed",
  "sequences": [
    {
      "protein": {
        "id": ["A"],
        "sequence": "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH"
      }
    }
  ],
  "modelSeeds": [1, 2, 3, 4, 5],
  "dialect": "alphafold3",
  "version": 1
}

Alternatively, use the --num_seeds flag in run_alphafold.py to auto-generate N seeds from a single seed.

RNA-Protein Complex

RNA chains are supported with nhmmer-based MSA search against RNAcentral, Rfam, and NT databases:

{
  "name": "rna_protein",
  "sequences": [
    {
      "protein": {
        "id": ["A"],
        "sequence": "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH"
      }
    },
    {
      "rna": {
        "id": ["B"],
        "sequence": "GGGGACUGCGUUCGCGCUUUCCCC"
      }
    }
  ],
  "modelSeeds": [1],
  "dialect": "alphafold3",
  "version": 3
}

DNA-Protein Complex

DNA chains pass through with empty MSA, matching AlphaFold 3's native behavior (AF3 does not perform MSA search for DNA):

{
  "name": "dna_protein",
  "sequences": [
    {
      "protein": {
        "id": ["A"],
        "sequence": "MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSH"
      }
    },
    {
      "dna": {
        "id": ["B", "C"],
        "sequence": "ACGTACGTACGT"
      }
    }
  ],
  "modelSeeds": [1],
  "dialect": "alphafold3",
  "version": 3
}

Batch Processing

Place multiple JSON files in a single directory and pass it as --input_dir:

inputs/
  protein_1.json
  protein_2.json
  protein_3.json

Each file is loaded as a separate fold input. When --batch_size is set, protein chains are collected and deduplicated across the loaded inputs, then grouped into efficient batched MMseqs2-GPU searches. Multiple protein chains from a single JSON file can therefore be searched in the same MMseqs2 batch.

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