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

Table 5

Relative performance among the four-body potential derived using a 4-letter alphabet and 12 Å cutoff as parameters and twelve other state-of-the-art methods.

	Native rank	-score		FE	Average of ranks	Overall ranking
4 letters/12 Å cutoff	47 (5)	17 (3)	8 (5)	27 (5)	4.5	3
Summa et al. [3]	97 (1)	44 (1)	7 (6)	19 (8)	4	2
United-atom vdW; (AMBER) [19]	25 (12)	0 (12)	4 (8)	10 (12)	11	12
Coulombic (AMBER) [19]	33 (8)	8 (6)	2 (11)	18 (9)	8.5	10
United-atom vdW + coulombic (AMBER) [19]	26 (11)	4 (9)	4 (8)	11 (11)	9.75	11
United-atom vdW (CHARM19) [20]	31 (10)	9 (4)	4 (8)	36 (3)	6.25	7
Coulombic (CHARM19) [20]	76 (2)	22 (2)	5 (7)	22 (7)	4.5	3
(Delarue and Koehl) [21]	70 (3)	7 (7)	0 (13)	17 (10)	8.25	9
(Koehl and Delarue) [22]	33 (8)	0 (12)	32 (2)	26 (6)	7	8
(Delarue and Koehl) [21]	20 (13)	1 (11)	1 (12)	9 (13)	12.25	13
RAPDF [23]	53 (4)	3 (10)	28 (3)	36 (3)	5	5
DFIRE [24]	38 (7)	9 (4)	33 (1)	51 (1)	3.25	1
Fogolari et al. [18]	40 (6)	5 (8)	15 (4)	39 (2)	5	5

Numbers not in parentheses in each column reflect how many decoy sets (out of 129) for which the given method matches the best performance value achieved among all 13 methods tested; numbers in parentheses are the rankings of the counts in that column; = correlation coefficient; FE = fractional enrichment.