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input.md 25.50 KiB

AlphaFold 3 Input

Specifying Input Files

You can provide inputs to run_alphafold.py in one of two ways:

  • Single input file: Use the --json_path flag followed by the path to a single JSON file.
  • Multiple input files: Use the --input_dir flag followed by the path to a directory of JSON files.

Input Format

AlphaFold 3 uses a custom JSON input format differing from the AlphaFold Server JSON input format. See below for more information.

The custom AlphaFold 3 format allows:

  • Specifying protein, RNA, and DNA chains, including modified residues.
  • Specifying custom multiple sequence alignment (MSA) for protein and RNA chains.
  • Specifying custom structural templates for protein chains.
  • Specifying ligands using Chemical Component Dictionary (CCD) codes.
  • Specifying ligands using SMILES.
  • Specifying ligands by defining them using the CCD mmCIF format and supplying them via the user-provided CCD.
  • Specifying covalent bonds between entities.
  • Specifying multiple random seeds.

AlphaFold Server JSON Compatibility

The AlphaFold Server uses a separate JSON format from the one used here in the AlphaFold 3 codebase. In particular, the JSON format used in the AlphaFold 3 codebase offers more flexibility and control in defining custom ligands, branched glycans, and covalent bonds between entities.