catalystforyou

Edit unsynthesizable, computationally-generated drug candidate molecules into synthesizable analogs that retain binding to a target protein pocket. Invoke when the user has SMILES from a 3D-aware generative model (Pocket2Mol, ResGen, TargetDiff, DiffSBDD, LIGAN, AR, or any de novo source) and asks for "synthesizable rescue", "make X synthesizable", "fix synthesis cliff", "edit to synthesizable", "lower SA score", or similar. The skill docks the inputs at the target pocket with AutoDock Vina, calls a reasoning LLM (Gemini-2.5-Pro, Gemini-3.1-Pro, or DeepSeek-V4-Pro) to predict atom-level edit sequences that preserve the PLIP interaction profile while removing synthesis liabilities, re-docks the edited products, and returns a ranked list of (original, edited, scores, similarity, reasoning) tuples. Use ONLY when the inputs are already-generated molecules and a defined receptor pocket exist. Do NOT use for: de novo generation, full retrosynthesis route planning, free-energy calculations, or covalent docking.