Table 2.

Comparison of prediction times between RGN2 and AF2, RF, and trRosetta across 330 targets spanning our orphan and de novo protein datasets. RGN2 predictions were performed in batches with maximum permissible batch size set to 128 targets. The trRosetta MSA generation step was not used since none of the targets had known homologous proteins.

Protein length (L) bins (# residues)	Total targets	Mean protein length (# residues)	Mean trRosetta prediction time per structure (s)		Mean AF2 prediction time (s)	Mean RF prediction time (s)	Mean RGN2 prediction time (ms)	Mean RGN2 prediction + refinement time (s)
			Distogram	3D-Structure
$0<L\le 100$	184	37.5	1768	1004	831.5	412.6	2.7	145.2
$100<L\le 200$	93	148.7	2791	1927	851.6	408.3	2.2	177.4
$200<L\le 300$	28	258.3	2877	1752	828.4	492.7	3.1	182.3
$300<L\le 400$	17	333.4	3647	2140	825.6	501.6	5.7	200.5
$400>L$	8	460.5	4012	3011	841.6	498.6	5.9	229.2