Refined AI-predicted Models with Ligands

This data record contains the energy minimized (relaxed) ligand-containing structures which are included in the relaxed AI-predicted models with ligands, but their refined version. Refinement includes, as described in the Methods section, the removal of low confidence regions with a pLDDT score below 70, and filtering for models with 10 or more amino-acid residues remaining. After refinement, ligands which are no longer within 5 Å of any atom in the model were removed. The included subfolders contain, as individual PDB files, 14,973 ligand-containing relaxed and refined AlphaFold 2 models, 15,070 ligand-containing relaxed and refined OpenFold models, and 12,855 ligand-containing relaxed and refined ESMFold models.