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PD-1 Targeted Antibody Discovery Using AI Protein Diffusion

Diffusion of Novel, PD-1-targeting Fab Structures with in silico Evaluation

Tuple, LLC

Journal Article

bioRxiv Preprint

Antibody Generation and Testing

Steps:

  1. Generate Sequences using EvoDiff
  2. Generate Structures using AlphaFold2 (TUPPD1-001 to TUPPD1-009)
  3. Prepare Structures
  4. Generate HADDOCK experiment files
  5. Submit HADDOCK experiments to HPC
    • Create Singularity container from Docker image: singularity build haddock.sif docker://cford38/haddock:2.4_36cores
    • Run experiment generation: bash ./scripts/4_experiment_submission/submit_experiments.sh
      • (Remember to chmod -R 755 the experiments/ folder so that Singularity can execute the scripts.)
  6. Collect best docked PDB structure and metrics for each experiment
  7. Clean up HADDOCK run files