Fig. 2. Screenshot of the AlphaFill entry page for cellular retinoic acid-binding protein 2 (AF-P29373).

The Mol* viewer on the left can be controlled by the table of transplanted compounds on the right. Clicking a compound in the table brings up a zoom of the binding site. Compounds can be hidden or shown individually using the tick boxes. Transplants at 70% or more sequence identity are displayed. The identity cutoff can be changed using the selector above the table. In this example, retinal (RET) inherited from PDB-REDO entry 4i9s (ref. ³⁶) is shown and flagged with a yellow box as medium confidence due to high TCS. All other transplanted compounds are hidden from view, providing the ‘optimize’ option for the selected transplant. After optimization (Supplementary Fig. 2) the is TCS is reduced to 0.29 Å, which is considered high confidence. A sodium from PDB-REDO entry 2frs (ref. ³⁷) is flagged for its high local r.m.s.d.