AF3 JSON Generator

This repository contains R scripts for generating AlphaFold3 input JSON files from a list of protein complexes and local FASTA sequences.

Usage

Rscript generate_json_AF3.R \
  -f ./human_seqs.fasta \
  -c ./test_complexes.csv \
  -b 30 \
  -o ./output_dir \
  -r ./failed_complexes.csv

Input format

The input file should be a .csv, where the 1st column is the name of the target complex. For example:

Complex
P00734-P00533
P00734-O75015
P00734-P00736
P00734-P02745

Just so you know, this version supports names with UNIPROT ID only, and should be separated by '-'.

Protein sequence

The current human_seqs.fasta contains the protein sequence of human from UniProt Reviewed (Swiss-Prot). You can also use your own .fasta using the -f.

Output

Each .json file in the output directory contains 30 complexes, which can be directly used for AF3 prediction. Use -b to change this number.