BindCraft Pipeline

A protein binder is a small, custom-built molecule designed to grab one target and hold on. Get the shape right and it can quiet a runaway disease pathway; get it wrong and it drifts past, useless. The hard part is the size of the search: the number of possible protein sequences is astronomically larger than the number of atoms in the observable universe, and almost all of them fold into nothing you'd want. Finding the rare few that grab the right target is the whole game.

BindCraft plays that game end to end — from picking a target protein, through generating binder candidates, to scoring how tightly each one should hold. Think of it as a conversation between two AI systems. One, RFDiffusion, imagines what a binder might look like: the shape that could nestle against the target. The other, ProteinMPNN, works backward to the amino acid sequence that would actually fold into that shape. ESM-2 embeddings give the models a feel for the language proteins are written in, and Rosetta's energy functions score the candidates, so the most promising ones move forward for experimental validation.

The immediate target is BAFF — B-cell activating factor — and miniprotein binders for Sjögren's syndrome, an autoimmune disease. The broader ambition is a disease-graph that connects proteins, pathways, and clinical endpoints across the rare disease landscape: eighteen targets cataloged so far, twenty-five structures mapped.

None of this runs without compute, and that is exactly the point. BindCraft runs on Lattice Protocol's federated GPU infrastructure, built on one stubborn commitment — compute should never be rare for the people working on rare disease. Every candidate that clears the pipeline is one someone can actually test: one more shape, one more shot at a target that used to have none. The code is open, the target list keeps growing, and the next binder is always the interesting one.