PI3K Docking and Virtual Screening

This repository documents a PI3K structural biology workflow, including docking validation, structural alignment, and virtual screening against human and fungal targets.

Compact Layout

• analysis/ - all workflow folders, notebooks, and analysis artifacts
• data/ - reference structures, images, FASTA files, and model outputs
• info.ipynb - main notebook that compiles the project narrative and results

Inside analysis/

• analysis/exercise_1/ - ligand and structure preparation for the first exercise
• analysis/exercise_2/ - file conversion and preparation utilities for docking inputs
• analysis/docking_comparisons/ - docking comparison against the crystallographic reference ligand
• analysis/structure_alignment/ - structural alignment, mutation analysis, and visualization
• analysis/fungal_docking/ - docking of fungal models against the selected ligands
• analysis/virtual_screening/ - virtual screening workflow and score comparison
• analysis/explanations/ - extra figures and explanation notebook material

Inside data/

• data/resources/ - source FASTA files and supporting reference material
• data/fungal_folding_models/ - homology-model outputs for the fungal protein
• data/images/ - figures used across the notebooks and reports
• data/pdbs/ - curated PDB structures and intermediate structural files
• data/docking/ - supporting ligand docking inputs

Main Files

• analysis/exercise_1/convert_sdf_to_pdb.sh - converts .sdf inputs to .pdb
• analysis/exercise_2/convert_txt_to_pdb.sh - converts ligand text files to .pdb
• analysis/structure_alignment/alignment/run_alignment_visualization.sh - runs the PI3K alignment visualization workflow
• analysis/virtual_screening/screening/run_screening.sh - runs the virtual screening pipeline with logs

Notes For GitHub

• The root is intentionally compact: the project content now lives under analysis/ and data/.
• The exercise numbering is preserved inside analysis/ because it matches the original project flow.
• The top-level tree is now easier to scan, while the scientific folders keep their original internal organization.