Runs N' Poses 2025.01: download

Runs N' Poses tests the ability of protein–ligand co-folding methods to generalize to systems different from those in their training set (Have protein-ligand co-folding methods moved beyond memorisation?; code on GitHub). CAMEO scores uploaded predictions against its data.

Modeling inputs

For each target, the protein chain sequences and the ligands (SMILES; 2025.01 also CCD codes): https://cameo3d.org/benchmarks/runs-n-poses/2025.01/download/inputs.json.The target list, with the numeric ids that uploads refer to, comes from the API (see the example code on the benchmark page).

Each protein chain has its sequence, one letter per residue, with modified residues given by their parent's letter or X. Where the target has modified residues, the chain also has a modifications list in AlphaFold 3's format (ptmType: the residue's CCD code; ptmPosition: its residue number, from 1). Tools that support modifications can model them. Either way, residues are numbered after sequence.

Other files

The ground truth (ground_truth.tar.gz) and the annotations (annotations.csv) are those of the original release, on Zenodo (the modeling inputs above are CAMEO's): https://zenodo.org/records/18366081 (version 6). They hold all 2,600 systems and every ligand; CAMEO scores the 2,579 systems that the annotations list, and only their proper ligands (ligand_is_proper). The target list, with each target's ligands, comes from the API.

The Runs N' Poses data is distributed under the Creative Commons Attribution 4.0 license (CC-BY-4.0).