Diverse effects of distance cutoff and residue interval on the performance of distance-dependent atom-pair potential in protein structure prediction

Table 3 Performance comparisons between the potentials we built and several widely-used statistical potentials

Decoy sets	Measurements	Dfire	RW	GOAP	ave-6-6^d	rw-17-3^e	Best^f
I-TASSER	R1-num^a	43	53	45	42	41	56 (6)
	Z-score^b	2.80	4.42	4.98	2.42	2.97	11.21 (dope-5-0)
	PCC^c	−0.47	−0.50	−0.50	−0.09	−0.51	−0.55 (rw-15/16–0)
Moulder	R1-num	18	19	19	19	19	20 (89)
	Z-score	2.67	2.78	3.48	2.97	2.75	8.17 (rw-8-0)
	PCC	−0.84	−0.83	−0.88	−0.52	−0.88	−0.89 (rw-16-2)
Rosetta	R1-num	22	20	45	41	18	48 (ave-8-14, srs-6-8)
	Z-score	1.55	1.48	3.38	3.11	1.46	3.56 (srs-6-7)
	PCC	−0.37	−0.36	−0.51	−0.31	−0.36	−0.45 (srs-6-13/15)
3DRobot	R1-num	1	0	94	176	19	184 (ave-5-5/6)
	Z-score	0.83	−0.30	1.85	3.19	1.16	3.50 (ave-5-5)
	PCC	−0.86	−0.85	−0.90	−0.70	−0.86	−0.88 (ave-19/20/21–5)
CASP10	R1-num	26	16	41	53	31	55 (ave-7-6/7/8)
	Z-score	0.76	0.86	1.60	1.34	1.31	1.70 (dope-6-10/11/12)
	PCC	−0.40	−0.41	−0.53	−0.22	−0.54	−0.56 (rw-18-3, rw-19-4)
CASP11	R1-num	24	15	37	47	33	49 (14)
	Z-score	0.82	1.01	1.91	1.37	1.50	1.72 (dope-6-11)
	PCC	−0.36	−0.40	−0.54	−0.23	−0.52	−0.52 (rw-17-3)
Total/Average	R1-num	134	123	281	378	161	378 (ave-6-6)
	Z-score	1.20	0.95	2.40	2.55	1.55	2.66 (dope-5-5)
	PCC	−0.60	−0.61	−0.68	−0.43	−0.66	−0.66 (rw-17/18–3)

^aThe number of decoy sets whose native structure is given the lowest energy score by the potential
^bDefined as (<E _decoy> − E _native)/δ, where E _nativeis the energy score of native structure, <E _decoy> and δare respectively the average and the standard deviation of energy scores of structural decoys
^cThe average Pearson’s correlation coefficient between the energy score and TM-score of all structures in each decoy set, including the native structure
^dThe potential based on the averaging reference state with both distance cutoff and residue interval to be 6
^eThe potential based on the random-walk chain reference state with distance cutoff = 17 and residue interval = 3
^fThe best values among the results of all 1728 potentials with different reference states, distance cutoffs and residue intervals. The corresponding potentials that achieve this values are given in parentheses (e.g. rw-15/16–0 means the potentials rw-15–0 and rw-16-0). Only the number of potentials is given in parentheses if more than 3 potentials can achieve the best value

ISSN: 1471-2105