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

Table 6

Overall rankings by separately comparing each four-body potential with twelve other methods.

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
Four-body potential	10	4	3	3	12	11	12	11	11	9	10	11
Summa et al. [3]	2	2	2	2	2	2	2	2	2	2	2	2
United-atom vdW (AMBER) [19]	12	12	12	12	11	12	11	12	12	12	12	12
Coulombic (AMBER) [19]	9	10	10	9	9	9	9	9	9	9	9	9
United-atom vdW + coulombic (AMBER) [19]	11	11	11	11	10	10	10	10	10	11	11	10
United-atom vdW (CHARM19) [20]	6	7	7	7	6	6	6	6	6	6	6	6
Coulombic (CHARM19) [20]	3	3	3	3	3	3	3	2	3	2	3	2
ΔE (Delarue and Koehl) [21]	8	9	9	10	8	8	8	8	8	8	8	8
(Koehl and Delarue) [22]	7	8	8	8	7	7	7	7	7	7	7	7
(Delarue and Koehl) [21]	13	13	13	13	12	13	13	13	13	13	13	13
RAPDF [23]	5	5	5	5	5	5	5	5	5	5	5	5
DFIRE [24]	1	1	1	1	1	1	1	1	1	1	1	1
Fogolari et al. [18]	4	5	5	5	4	4	4	4	4	4	4	4

Note that the overall rankings in this column correspond to those in the final column of Table 5; the remaining columns in this table were obtained by repeating the data analyses that generated Table 5 with respect to each of the other 11 four-body potentials.