Data for "Influence of molecular representation and charge on protein-ligand structural predictions by popular co-folding methods"

Models generated in the "Influence of molecular representation and charge on protein-ligand structural predictions by popular co-folding methods" Models are first grouped into folders by the target protein, then tool, then ligand and input format. Ligands predicted with Chai-1 are always specified with SMILES. Structures generated by AlphaFold 3 that do not include the word 'sample' in the filename were not present in the analysis. AlphaFold 3 structures used for analysis had seeds 10, 11, 12, 13, 14, 15, 16, 17, 18, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190