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Overview

AlphaFold 3 uses a custom JSON input format that provides extensive control over structure prediction. You can provide inputs in two ways:

Single Input

Use --json_path flag with a single JSON file

Multiple Inputs

Use --input_dir flag with a directory of JSON files

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Key Capabilities

The AlphaFold 3 JSON format allows you to:
  • Specify protein, RNA, and DNA chains with modified residues
  • Provide custom multiple sequence alignments (MSA) for proteins and RNA
  • Include custom structural templates for proteins
  • Define ligands using CCD codes, SMILES, or custom definitions
  • Specify covalent bonds between entities
  • Control predictions with multiple random seeds

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Top-Level Structure

Every AlphaFold 3 input JSON file follows this structure: 
{
  "name": "Job name goes here",
  "modelSeeds": [1, 2],
  "sequences": [
    {"protein": {...}},
    {"rna": {...}},
    {"dna": {...}},
    {"ligand": {...}}
  ],
  "bondedAtomPairs": [...],
  "userCCD": "...",
  "dialect": "alphafold3",
  "version": 4
}

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Required Fields

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name
string
required
The name of the job. A sanitized version is used for output file naming.
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modelSeeds
array<integer>
required
List of integer random seeds. You must provide at least one seed. Each seed generates one predicted structure.
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sequences
array
required
List of molecular entities (proteins, RNA, DNA, ligands). See detailed specifications in the JSON Specification guide.
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dialect
string
required
Must be set to "alphafold3"
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version
integer
required
Must be set to 1, 2, 3, or 4. Version 4 is the latest.

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Optional Fields

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bondedAtomPairs
array
Specifies covalent bonds between entities. Used for covalent ligands and multi-CCD ligands like glycans.
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userCCD
string
User-provided chemical components dictionary in CCD mmCIF format (inline). Mutually exclusive with userCCDPath.
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userCCDPath
string
Path to file containing user-provided CCD. Mutually exclusive with userCCD.

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Format Versions

The input format has evolved across versions:
1

Version 1

Initial AlphaFold 3 input format with basic entity definitions
2

Version 2

Added unpairedMsaPath, pairedMsaPath, and mmcifPath fields for external MSA and templates
3

Version 3

Added userCCDPath field for external user-provided CCD
4

Version 4

Added description field for textual descriptions of chains and ligands

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AlphaFold Server Compatibility

The AlphaFold 3 codebase uses a different JSON format from AlphaFold Server. However, run_alphafold.py includes an automatic converter that detects and translates AlphaFold Server JSON format.

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Key Differences

FeatureAlphaFold ServerAlphaFold 3
Multiple inputsList at top levelOne input per file
IonsSeparate entity typeTreated as ligands
Entity IDsAuto-assignedUser-specified (required)
GlycansSupportedMust convert manually

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Multiple Inputs

The AlphaFold Server format allows multiple inputs in a single JSON (top-level list). The AlphaFold 3 format requires one input per file. The converter handles this automatically.

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Random Seeds

If AlphaFold Server JSON specifies "modelSeeds": [], the converter randomly chooses a seed. AlphaFold 3 format always requires explicit seeds.

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Entity IDs

AlphaFold Server doesn’t require entity IDs. The converter auto-assigns IDs in “reverse spreadsheet style”: 
A, B, ..., Z, AA, BA, CA, ..., ZA, AB, BB, CB, ..., ZB, ...

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Quick Example

Here’s a minimal valid input for a homodimer protein:
fold_input.json
{
  "name": "2PV7",
  "sequences": [
    {
      "protein": {
        "id": ["A", "B"],
        "sequence": "GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQANDLKQG"
      }
    }
  ],
  "modelSeeds": [1],
  "dialect": "alphafold3",
  "version": 1
}

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Next Steps

JSON Specification

Detailed entity definitions and examples

Running Docker

Execute AlphaFold 3 with your input files

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