Table 2:

Results from 100 trials of our “leave-10%-out” model robustness test for binding (A) and folding (B). The feature is indicated by the first column. The second column indicates the average rank across all trials the given feature appeared in, lower numbers suggest more robust features. The third column shows the standard error associated with the average. The fourth column indicates the average ΔR² from all trials the feature appeared in (higher numbers suggest more robustness), the fifth column indicates the total number of trials a given feature occurred in out of 100 possible, the sixth column indicates whether the feature was present in the full model, and the last column indicates the rank of the feature in the full model.

2A Binding Validation
Feature	Mean Rank	Mean Rank SE	Average ΔR2	Number of Models (/100)	In Full Model	Full Model Rank
Complex Type	1.04	0.02	0.134	100	Yes	1
Charge	2.01	0.036	0.082	100	Yes	2
Separation	3.66	0.118	0.0560	100	Yes	3
Sizenet	4.45	0.097	0.047	100	Yes	5
Interaction side	4.66	0.118	0.046	100	Yes	4
SASA	5.64	0.097	0.0380	100	Yes	6
Secondary Structure	6.68	0.087	0.022	97	Yes	7
Hydrophobicity	7.469	0.018	0.018	32	No	N/A
2B Folding Validation
Feature	Mean Rank	Mean Rank SE	Average ΔR2	Number of Models (/100)	In Full Model	Full Model Rank
Hydrophobicity	1.212	0.062	0.15	99	Yes	1
Charge	3.083	0.122	0.082	96	Yes	3
SecondaryStructure	3.213	0.164	0.0810	47	Yes	N/A
Sizenet	3.22	0.127	0.074	100	Yes	2
Separation	3.98	0.126	0.058	100	Yes	4
SASA	4.897	0.092	0.041	97	Yes	5
Number Residues	5.269	0.113	0.0380	26	No	N/A