Preparation of structures (AlphaFold/Multimer), assess confidence, and clean targets/ligands

binding sites, generate grids and constraints where relevant

Standardized ligand libraries (SDF/SMILES), protonation/tautomer states, and minimization

Docking (e.g., AutoDock-GPU/Vina) with ranking and quick rescoring

Contacts interfaces and hotspots and epitope triage

Protein design: from binders to upgraded proteins

Summarized decisions with pose galleries and rationale for selections

PDBs, SDFs, PyMOL sessions, and a one-page decision brief with next steps