All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds

Table 4

Relative performance among twelve atomic four-body statistical potentials.

Alphabet size	4	4	4	4	8	8	8	8	20	20	20	20
Cutoff (Å)	4.8	8	12	None	4.8	8	12	None	4.8	8	12	None
Native rank	42	48	55	61	23	29	27	25	33	41	34	33
	(4)	(3)	(2)	(1)	(12)	(9)	(10)	(11)	(7)	(5)	(6)	(7)
-score	25	9	18	37	1	4	1	1	15	21	2	11
	(2)	(7)	(4)	(1)	(10)	(8)	(10)	(10)	(5)	(3)	(9)	(6)
	10	9	6	24	4	6	7	9	5	28	21	16
	(5)	(6)	(9)	(2)	(12)	(9)	(8)	(6)	(11)	(1)	(3)	(4)
FE	38	46	49	47	23	34	32	38	37	56	43	42
	(7)	(4)	(2)	(3)	(12)	(10)	(11)	(7)	(9)	(1)	(5)	(6)
Average of ranks	4.5	5	4.25	1.75	11.5	9	9.75	8.5	8	2.5	5.75	5.75
Overall ranking	4	5	3	1	12	10	11	9	8	2	6	6

Numbers above parentheses in each row reflect how many decoy sets (out of 145) for which the given potential matches the best performance value achieved among all 12 potentials tested; numbers in parentheses are the rankings of the counts in that row; = correlation coefficient; FE = fractional enrichment.