A new model designs proteins atom by atom, not just backbone first.

Proteins are tiny molecular machines that do work inside living cells. Designing new ones is hard. Most computer methods split the task into separate steps or avoid working with all the atoms directly in normal physical space. To fix this, researchers built PANDA. It is a new system that generates whole proteins end-to-end. It cleans up noisy all-atom shapes directly in coordinate space and reads out the protein's chemical sequence from where its atoms sit. It links global and local coordinate tracks while keeping side-chain shapes intact. PANDA scored the highest self-consistency design success across protein lengths among tested all-atom tools. For functional proteins, it holds motif distances flexible, achieving much higher scaffolding success on an enzyme benchmark, especially on larger motifs.

Why it matters

Designing new proteins usually happens in stages—first the backbone shape, then the amino acid sequence—which can miss how side chains actually fit. PANDA designs every atom at once, so the final protein is more likely to fold correctly. This could speed up creating custom enzymes or therapeutic proteins.

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