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

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

Decoy sets Measurements Dfire RW GOAP ave-6-6d rw-17-3e Bestf
I-TASSER R1-numa 43 53 45 42 41 56 (6)
Z-scoreb 2.80 4.42 4.98 2.42 2.97 11.21 (dope-5-0)
PCCc −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)
  1. aThe number of decoy sets whose native structure is given the lowest energy score by the potential
  2. 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
  3. cThe average Pearson’s correlation coefficient between the energy score and TM-score of all structures in each decoy set, including the native structure
  4. dThe potential based on the averaging reference state with both distance cutoff and residue interval to be 6
  5. eThe potential based on the random-walk chain reference state with distance cutoff = 17 and residue interval = 3
  6. 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