- Generate Sequences using EvoDiff
- Follow EvoDiff logic in
scripts/0_sequence_generation/EvoDiff_sequence_generation.md
- Follow EvoDiff logic in
- Generate Structures using AlphaFold2 (TUPPD1-001 to TUPPD1-009)
- Run AlphaFold2 Batch using
scripts/1_structure_generation/AlphaFold2_batch.ipynb
- Run AlphaFold2 Batch using
- Prepare Structures
- Renumber L chains in PDB files with PyMol:
scripts/2_structure_prep/PDB_renumberer.ipynb - Detect CDR loop residues:
scripts/2_structure_prep/fab_cdr_detection.ipynb
- Renumber L chains in PDB files with PyMol:
- Generate HADDOCK experiment files
- Run experiment generation using
scripts/3_experiment_generation/make_HADDOCK_experiments.ipynb
- Run experiment generation using
- 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 755theexperiments/folder so that Singularity can execute the scripts.)
- (Remember to
- Create Singularity container from Docker image:
- Collect best docked PDB structure and metrics for each experiment
- Run experiment metrics collection:
scripts/5_metrics_collection/postprocessing.ipynb- This notebook also runs PRODIGY to calculate binding affinities for each structure.
- Run experiment metrics collection:
- Clean up HADDOCK run files
- Run cleanup to move each experiments' run1/ directory into outputs:
scripts/6_cleanup/cleanup.ipynbX. Run various post-analyses: - abYsis for analyzing the residues in the Fabs:
analysis/abysis - OpenMM for molecular dynamics of the docked structures:
analysis/molecular_dynamics/run_openmm.ipynb
- Run cleanup to move each experiments' run1/ directory into outputs: