peptides that don't work
simulating peptide changes, and what compounds will not work with the bounding pockets.
Core trick
Computes pocket electrostatics on a protein surface, then uses ESM-2 to design peptides with complementary charge.
Description
simulating peptide changes, and what compounds will not work with the bounding pockets.
The bench loads a protein structure, finds the pockets on its surface, and proposes peptides that should fit: designing new ones, and searching 17,000 real catalogued ones, scored on the same objective so you can see which wins. You drive it in plain English — one question, and GPT-6 Astra calls the tools, runs the physics, and pulls trial results for drugs already approved against that target.
README excerpt
# Steering bench Ask a protein where its field will carry a charged molecule, then have a language model design one that goes there. Load any structure by PDB id or UniProt accession. The bench finds its pockets, computes the electrostatic field around it, releases test charges and shows which ones get funnelled onto the surface. Then ESM-2 designs a peptide whose charge is complementary to a chosen pocket, held to something protein-like by the model's own likelihood. The loop is **generate → predict → explain**: the model proposes, the physics says whether the field would actually steer it in, and the funnel on screen is the reason why. ## Run it ```bash python3 server.py # then open http://127.0.0.1:8020 ``` Needs `numpy`, `scipy`, `scikit-image`, and `transformers` + `torch` for the design panel. No API key. Nothing is downloaded except the structure you ask for. Try `P00441` (superoxide dismutase). It is a net-negative protein and steers a positive probe hard: **96% capture**. Press **Reverse** to flip its acidic residues and capture falls to **0%**. That is the demo.  *Trypsin. The field lines on the right funnel a positive probe onto the surface; the gold box is a detected pocket with its confidence. Nothing here needs a model or a key.* ## What runs on what | Stage | Engine | Needs | |---|---|---| | Structure fetch | AlphaFold DB / RCSB | network | | Pocket detection | buriedness on a grid, LIGSITE-style | nothing | | Fiel