1. Alphafold3 JSON Input Generator

generate_af3_inputs.py - Complete AlphaFold3 JSON input generator

Input JSONs (when using 8 sequences)

• Set 1 (PRTases): 64 files (8 sequences × 8 scenarios)
• Set 2 (TCA): 96 files (8 sequences × 6 substrates × 2 assemblies)
• Set 3 (nucleotide): 64 files (8 sequences × 8 substrates)
• Total: 224 JSON input files

2. Analysis Scripts

analyze_af3_results_combined.py - Comprehensive analysis for all AF3 outputs

• Generates heatmaps with overall pLDDT values

• Extracts metrics: ipTM, pLDDT, PAE, contact probability

  plot_ligand_pae_bars.py - Ligand:Contact residues PAE analysis for GAGA.

• Plotting and statistics for GAGA dimer predictions

extract_ligand_contacts.py - Ligand contact residue extraction

• Extracts residues within 5 Å (or custom distance) of all ligands
• Generates single CSV file with two columns: structure name and contact residues
• Residue format: chain:number:type (e.g., "A:37:ARG, B:53:ARG")
• Handles all ligand types: substrates, Mg²⁺, cofactors

3. Visualization

visualize_structures.py - Publication-ready PyMOL visualization

• Automatic ligand detection and coloring
• CMYK-safe colors
• Mesh surfaces around ligands
• Contact residue highlighting (5 Å threshold)
• Ray-tracing