README.md

Large-Scale Computational Modeling of H5 Influenza Variants Against HA1-Neutralizing Antibodies

Colby T. Ford, Shirish Yasa, Khaled Obeid, Rafael Jaimes III, Phillip J. Tomezsko,
Sayal Guirales-Medrano, Richard Allen White III, and Daniel Janies

Data

Outputs:

• Docking metrics, antigen/antibody metadata, and clustering results: Experiments.xlsx
• Docked structures ($n=1,804$): data/results
• Phylogenetic Tree: tree0.tnt.nex

Inputs:

• Antigens ($n=164$):
  • Input Sequences: data/sequences
  • Predicted Structures: data/structures/antigens/HA1
• Antibodies ($n=11$):
  • Structures: data/structures/antibodies

Workflow

Scripts

0. Sequence Collection: 0_sequence_collection
1. Structure Generation with ColabFold: 1_structure_generation
2. PDB Structure Preparation: 2_structure_prep
3. HADDOCK3 Experiment Generation: 3_experiment_generation
4. HPC Experiment Submission: 4_experiment_submission
5. Cleanup: 5_cleanup
6. Metrics Collection: 6_metrics_collection
7. Analyses: 7_analyses
   • Statistics: 7_analyses/statistics
   • Structure Analyses: 7_analyses/statistics
   • Phylogenetics: 7_analyses/phylogenetics
   • GIRAF Graph Analyses: scripts/7_analyses/giraf