> ## Documentation Index
> Fetch the complete documentation index at: https://mintlify.com/google-deepmind/alphafold3/llms.txt
> Use this file to discover all available pages before exploring further.

# Input File Format

> Overview of AlphaFold 3 input JSON format and specifications

## Overview

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

<CardGroup cols={2}>
  <Card title="Single Input" icon="file">
    Use `--json_path` flag with a single JSON file
  </Card>

  <Card title="Multiple Inputs" icon="folder">
    Use `--input_dir` flag with a directory of JSON files
  </Card>
</CardGroup>

## 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

## Top-Level Structure

Every AlphaFold 3 input JSON file follows this structure:

```json theme={null}
{
  "name": "Job name goes here",
  "modelSeeds": [1, 2],
  "sequences": [
    {"protein": {...}},
    {"rna": {...}},
    {"dna": {...}},
    {"ligand": {...}}
  ],
  "bondedAtomPairs": [...],
  "userCCD": "...",
  "dialect": "alphafold3",
  "version": 4
}
```

### Required Fields

<ParamField path="name" type="string" required>
  The name of the job. A sanitized version is used for output file naming.
</ParamField>

<ParamField path="modelSeeds" type="array<integer>" required>
  List of integer random seeds. You must provide at least one seed. Each seed generates one predicted structure.
</ParamField>

<ParamField path="sequences" type="array" required>
  List of molecular entities (proteins, RNA, DNA, ligands). See detailed specifications in the [JSON Specification](/guides/json-specification) guide.
</ParamField>

<ParamField path="dialect" type="string" required>
  Must be set to `"alphafold3"`
</ParamField>

<ParamField path="version" type="integer" required>
  Must be set to `1`, `2`, `3`, or `4`. Version 4 is the latest.
</ParamField>

### Optional Fields

<ParamField path="bondedAtomPairs" type="array">
  Specifies covalent bonds between entities. Used for covalent ligands and multi-CCD ligands like glycans.
</ParamField>

<ParamField path="userCCD" type="string">
  User-provided chemical components dictionary in CCD mmCIF format (inline). Mutually exclusive with `userCCDPath`.
</ParamField>

<ParamField path="userCCDPath" type="string">
  Path to file containing user-provided CCD. Mutually exclusive with `userCCD`.
</ParamField>

## Format Versions

The input format has evolved across versions:

<Steps>
  <Step title="Version 1">
    Initial AlphaFold 3 input format with basic entity definitions
  </Step>

  <Step title="Version 2">
    Added `unpairedMsaPath`, `pairedMsaPath`, and `mmcifPath` fields for external MSA and templates
  </Step>

  <Step title="Version 3">
    Added `userCCDPath` field for external user-provided CCD
  </Step>

  <Step title="Version 4">
    Added `description` field for textual descriptions of chains and ligands
  </Step>
</Steps>

## AlphaFold Server Compatibility

<Note>
  The AlphaFold 3 codebase uses a different JSON format from [AlphaFold Server](https://alphafoldserver.com). However, `run_alphafold.py` includes an automatic converter that detects and translates AlphaFold Server JSON format.
</Note>

### Key Differences

| Feature         | AlphaFold Server     | AlphaFold 3               |
| --------------- | -------------------- | ------------------------- |
| Multiple inputs | List at top level    | One input per file        |
| Ions            | Separate entity type | Treated as ligands        |
| Entity IDs      | Auto-assigned        | User-specified (required) |
| Glycans         | Supported            | Must convert manually     |

### 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.

### Random Seeds

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

### Entity IDs

AlphaFold Server doesn't require entity IDs. The converter auto-assigns IDs in "reverse spreadsheet style":

```text theme={null}
A, B, ..., Z, AA, BA, CA, ..., ZA, AB, BB, CB, ..., ZB, ...
```

## Quick Example

Here's a minimal valid input for a homodimer protein:

```json fold_input.json theme={null}
{
  "name": "2PV7",
  "sequences": [
    {
      "protein": {
        "id": ["A", "B"],
        "sequence": "GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQANDLKQG"
      }
    }
  ],
  "modelSeeds": [1],
  "dialect": "alphafold3",
  "version": 1
}
```

## Next Steps

<CardGroup cols={2}>
  <Card title="JSON Specification" icon="brackets-curly" href="/guides/json-specification">
    Detailed entity definitions and examples
  </Card>

  <Card title="Running Docker" icon="docker" href="/guides/running-docker">
    Execute AlphaFold 3 with your input files
  </Card>
</CardGroup>