How-Do-You-Do-It: Analyzing AlphaFold predictions with ChimeraX

This repository contains scripts and tutorials prepared for the How-do-you-do-it series at the Vienna BioCenter on analyzing AlphaFold predictions using ChimeraX.

Overview

• Tutorial Folder:
  Contains an HTML file that provides a step-by-step tutorial on how to analyse of AlphaFold predictions with ChimeraX.

• Python Folder:
  Contains a script to generate AlphaFold missense coloring commands for multi-chain PDBs or for UniProt IDs and can not be directly run in ChimeraX.

Quick Start

The fastest way to visualize your AlphaFold prediction is to download the analysis scripts from here and follow the instructions in the README files for installation. The installation is straightforward!

The scripts will:

• Load the five predictions from an AlphaFold run.
• Associate the JSON file to each prediction.
• Identify interface residues and write them to files.
• Generate a slider to easily browse through and compare the different predictions.

Separate scripts (with identical functionality) are available to support the file formats generated by:

• The AlphaFold 3 web server
• The results of an AlphaFold 2 screen as implemented by Dominik Handler (analyzes one hit at a time)
• The auto-alphafold.sh script by Juraj Ahel

Matthias Vorländer, January 2025, VBC
matthias.vorlaender@imp.ac.at A big thanks to the ChimeraX team for answering my many questions!!