Table 9.

Denoising distances at various levels of noise for the ubiqutin (PDG 1d3z, [19]). η̄_SDP,GOOD denotes the average noise of the hard constraint (‘good’) distances after the SDP embeddings. Note that the current implementation of the SNL-SDP algorithm used for the patch embeddings does not allow for hard distance constraints

				Existing distances				Missing distances
η (%)	${\overline{\text{ANE}}}_{\text{old}}$	${\overline{\text{ANE}}}_{\text{new}}$	η̄	η̄SDP	η̄SDP,GOOD	η̄MDA	η̄SDP	η̄MDA
0	0.00048	0.00039	0	0.02	0.14	0	0.38	0.32
10	0.00316	0.00266	4.91	3.42	1.79	3.13	3.2	2.99
20	0.00590	0.00506	9.81	7.01	3.68	6.44	6.18	5.81
30	0.00957	0.00803	14.74	10.75	5.59	9.88	9.51	8.95
40	0.01292	0.01120	19.65	14.5	7.62	13.42	13.55	12.8
50	0.01639	0.01462	24.57	18.1	9.82	16.93	18.24	17.35