Geodesic's NovaAtom-Lite tops FoldBench with 79.07% antibody-antigen success, beating AlphaFold 3
QuanquanGu · x · 2026-11-11
Geodesic Intelligence, founded by former SeedFold technical lead Quanquan Gu, released NovaAtom-Lite, an all-atom structure prediction model that predicts every heavy atom position for protein, DNA and RNA assemblies plus bound ligands, with per-residue and pairwise confidence.
Key FoldBench results (5 seeds × 5 samples, top-1 by its own ranking score, same 2021-09-30 training cutoff as AlphaFold 3):
- Antibody-antigen: 79.07% (n=172) vs IsoDDE 75.58% and AlphaFold 3's 47.90%
- Protein-ligand: 77.06% vs IsoDDE 75.99% and AlphaFold 3's 64.90%
- Also leads on protein monomer (LDDT 0.891), protein-protein (75.63%) and RNA monomer (0.620); trails on protein-DNA (74.24% vs AlphaFold 3's 79.18%)
- On PDB 8IDO (MERS-CoV RBD nanobody, released 2024, post-cutoff), all 25 predictions docked correctly, top-1 DockQ 0.839
Live now via the Geodesic API and NovaDDE. The team frames its edge as being exactly at the interfaces drug discovery cares about: antibody-antigen and protein-small-molecule.
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