AlphaFold3-GUI

AlphaFold3-GUI is a Streamlit app for building AlphaFold 3 input JSON files, including optional covalent ligand workflows from SMILES input.

It is designed for users who want a guided interface instead of manually editing JSON and mmCIF content.

Features

• Build AlphaFold 3 input JSON for proteins, RNA, DNA, and ligands
• Add multiple copies of entities with automatic label assignment (A, B, C, ...)
• Enter polymer modifications/templates as JSON arrays
• Generate covalent ligand userCCD content from a SMILES-derived ligand structure
• Download the generated JSON directly from the UI

Quick Start

Prerequisites

• Python 3.8+
• AlphaFold 3 installed/configured separately (this repo only generates inputs)
• Dependencies from requirements.txt

Install

git clone https://github.com/sieber-lab/AlphaFold3-GUI.git
cd AlphaFold3-GUI
pip install -r requirements.txt

Notes:

• rdkit installation can be platform-dependent. If pip install fails, install RDKit via conda/mamba and then install the remaining requirements.

Run

streamlit run streamlit_app.py

Usage Guide

1. Job Details

• Set a job name (used in the JSON and download filename)
• Enter model seeds as comma-separated integers (invalid values are ignored with a warning)

2. Entity Counts

• Choose how many protein, RNA, DNA, and ligand entities to add
• The app will create input sections for each entity

3. Fill Entity Inputs

• Protein / RNA / DNA: add sequences and optional modifications
• Ligand: add a SMILES string or use the covalent workflow

4. Optional Covalent Ligand Workflow

The covalent workflow helps create a custom ligand and bond definition:

1. Render the ligand from SMILES
2. Define the leaving group (by bond indices or atom list)
3. Choose the ligand atom that will remain bound
4. Choose the protein/RNA/DNA entity and residue
5. Enter the target atom name (CCD atom name on the biomolecule side)
6. Finalize the bond to generate userCCD data

5. Generate and Download JSON

• Click Generate JSON
• Review the JSON preview in the app
• Click Download JSON and use the file as AlphaFold 3 input

Current Limitations

• Covalent ligand mode currently supports one ligand with one copy at a time
• The app validates common input issues, but it does not fully validate every AlphaFold 3 schema rule
• userCCD export currently uses a single generated ligand definition

Repository Layout

• streamlit_app.py — Streamlit UI and input flow
• utils.py — JSON generation and ligand/mmCIF conversion helpers
• seqs.py — sequence data model classes
• requirements.txt — Python dependencies
• monomers.cif — reference monomer definitions used by the project

Troubleshooting

• RDKit errors while rendering a ligand

  • Check the SMILES string
  • Try a simpler ligand first
  • Some molecules may fail 3D embedding/optimization

• Covalent options unavailable

  • Ensure at least one protein/RNA/DNA entity is defined
  • Use exactly one ligand with one copy for covalent mode

• Invalid JSON array fields

  • Use valid JSON arrays such as [], [{"ptmType":"..."}], or [{"template":"..."}]

License

This project is licensed under the Apache License. See LICENSE.