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Entity Types

AlphaFold 3 supports four primary entity types in the sequences array:

Protein

Amino acid sequences with modifications and templates

RNA

RNA sequences with modifications and MSA

DNA

DNA sequences with modifications

Ligand

Small molecules via CCD codes or SMILES

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Protein Entities

Proteins are the most feature-rich entity type, supporting MSA, templates, and modifications.

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Basic Structure

{
  "protein": {
    "id": "A",
    "sequence": "PVLSCGEWQL",
    "modifications": [
      {"ptmType": "HY3", "ptmPosition": 1},
      {"ptmType": "P1L", "ptmPosition": 5}
    ],
    "description": "10-residue protein with 2 modifications",
    "unpairedMsa": null,
    "pairedMsa": null,
    "templates": []
  }
}

​
Field Specifications

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id
string | array<string>
required
Uppercase letter(s) for unique chain ID. Use array for homomers: ["A", "B", "C"]
​
sequence
string
required
Amino acid sequence using 1-letter standard codes
​
modifications
array
Post-translational modifications. Each has ptmType (CCD code) and ptmPosition (1-based)
​
description
string
Optional textual description (version 4+)
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unpairedMsa
string
A3M format MSA or empty string. Mutually exclusive with unpairedMsaPath
​
unpairedMsaPath
string
Path to A3M MSA file (absolute or relative to JSON)
​
pairedMsa
string
A3M format paired MSA. Recommended to use unpairedMsa instead
​
pairedMsaPath
string
Path to paired MSA file
​
templates
array
Structural templates in mmCIF format with alignment mappings

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Homodimer Example

{
  "protein": {
    "id": ["A", "B"],
    "sequence": "MKLLVVSGGSGS",
    "description": "Homodimer with two copies"
  }
}

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With Custom MSA

{
  "protein": {
    "id": "A",
    "sequence": "DEEP",
    "unpairedMsa": ">query\nDEEP\n>match1\nD--P\n>match2\nDD-P",
    "pairedMsa": "",
    "templates": []
  }
}

​
RNA Entities

RNA sequences support modifications and MSA. 
{
  "rna": {
    "id": "E",
    "sequence": "AGCU",
    "modifications": [
      {"modificationType": "2MG", "basePosition": 1},
      {"modificationType": "5MC", "basePosition": 4}
    ],
    "description": "4-base RNA with modifications",
    "unpairedMsa": null
  }
}

​
Field Specifications

​
id
string | array<string>
required
Uppercase letter(s) for chain ID
​
sequence
string
required
RNA sequence using only A, C, G, U
​
modifications
array
Each has modificationType (CCD code) and basePosition (1-based)
​
unpairedMsa
string
A3M format MSA
​
unpairedMsaPath
string
Path to MSA file

​
DNA Entities

DNA sequences support modifications but not MSA or templates. 
{
  "dna": {
    "id": "C",
    "sequence": "GACCTCT",
    "modifications": [
      {"modificationType": "6OG", "basePosition": 1},
      {"modificationType": "6MA", "basePosition": 2}
    ],
    "description": "7-base DNA strand"
  }
}

​
Field Specifications

​
id
string | array<string>
required
Uppercase letter(s) for chain ID
​
sequence
string
required
DNA sequence using only A, C, G, T
​
modifications
array
Each has modificationType (CCD code) and basePosition (1-based)

​
Ligand Entities

Ligands can be specified three ways: 
{
  "ligand": {
    "id": ["F", "G", "H"],
    "ccdCodes": ["ATP"],
    "description": "Three ATP molecules"
  }
}
Use standard Chemical Component Dictionary codes. Supports covalent bonds to other entities.

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Field Specifications

​
id
string | array<string>
required
Uppercase letter(s) for ligand ID
​
ccdCodes
array<string>
List of CCD codes (standard or custom). Mutually exclusive with smiles
​
smiles
string
SMILES definition. Mutually exclusive with ccdCodes

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SMILES JSON Escaping

Backslashes in SMILES must be escaped. Use jq or Python to properly escape:
jq -R . <<< 'CCC[C@@H](O)CC\C=C\C=C\C#CC#C\C=C\CO'

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Ions as Ligands

Ions are treated as ligands. For example, a magnesium ion:
{
  "ligand": {
    "id": "MG1",
    "ccdCodes": ["MG"]
  }
}

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Structural Templates

Templates are only supported for proteins. 
"templates": [
  {
    "mmcif": "data_template\n_entry.id template\n...",
    "queryIndices": [0, 1, 2, 4, 5, 6],
    "templateIndices": [0, 1, 2, 3, 4, 8]
  }
]
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mmcif
string
Single-chain protein template in mmCIF format. Mutually exclusive with mmcifPath
​
mmcifPath
string
Path to mmCIF file (can be gzip, xz, or zstd compressed)
​
queryIndices
array<integer>
required
0-based indices in query sequence
​
templateIndices
array<integer>
required
0-based indices in template sequence (account for unresolved residues)
mmCIF files may have unresolved residues. These must be counted when specifying templateIndices.

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Covalent Bonds

Define bonds between or within entities using bondedAtomPairs: 
"bondedAtomPairs": [
  [["A", 145, "SG"], ["L", 1, "C04"]],
  [["J", 1, "O6"], ["J", 2, "C1"]]
]
Each bond is defined by two atoms: [entityId, residueId, atomName]
  • Entity ID: Chain ID from id field
  • Residue ID: 1-based position within chain
  • Atom name: From CCD definition

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Glycan Example

{
  "sequences": [
    {
      "protein": {
        "id": "A",
        "sequence": "...ASN..."
      }
    },
    {
      "ligand": {
        "id": "B",
        "ccdCodes": ["CMP1", "CMP2", "CMP3", "CMP4"]
      }
    }
  ],
  "bondedAtomPairs": [
    [["A", 42, "ND2"], ["B", 1, "C1"]],
    [["B", 1, "O4"], ["B", 2, "C1"]],
    [["B", 2, "O3"], ["B", 3, "C1"]],
    [["B", 2, "O6"], ["B", 4, "C1"]]
  ]
}

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Complete Example

Here’s a comprehensive input demonstrating multiple entity types: 
{
  "name": "Complex Structure",
  "modelSeeds": [10, 42],
  "sequences": [
    {
      "protein": {
        "id": "A",
        "sequence": "PVLSCGEWQL",
        "modifications": [
          {"ptmType": "HY3", "ptmPosition": 1},
          {"ptmType": "P1L", "ptmPosition": 5}
        ],
        "description": "Protein with modifications"
      }
    },
    {
      "protein": {
        "id": "B",
        "sequence": "RPACQLW",
        "templates": []
      }
    },
    {
      "dna": {
        "id": "C",
        "sequence": "GACCTCT",
        "modifications": [
          {"modificationType": "6OG", "basePosition": 1}
        ]
      }
    },
    {
      "rna": {
        "id": "E",
        "sequence": "AGCU",
        "modifications": [
          {"modificationType": "2MG", "basePosition": 1}
        ]
      }
    },
    {
      "ligand": {
        "id": ["F", "G", "H"],
        "ccdCodes": ["ATP"]
      }
    },
    {
      "ligand": {
        "id": "Z",
        "smiles": "CC(=O)OC1C[NH+]2CCC1CC2"
      }
    }
  ],
  "bondedAtomPairs": [
    [["A", 1, "CA"], ["G", 1, "CHA"]]
  ],
  "dialect": "alphafold3",
  "version": 4
}

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Next Steps

Input Format

Top-level structure overview

Output Format

Understanding prediction outputs

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