All-Atom Four-Body Knowledge-Based Statistical Potentials to Distinguish Native Protein Structures from Nonnative Folds
Table 3
Performance evaluation on 145 benchmarks in 8 decoy sets from Decoys-‘R’-Us, based on energies obtained with the four-body potential derived using a 4-letter alphabet and 12 Å cutoff as parameters.
Decoy set
PDB ID
Native rank
-score
FE
4state_reduced
1ctf
156/631
0.7
0.27
11.1
1r69
6/676
2.5
0.18
14.9
1sn3
23/660
1.8
0.42
48.5
2cro
5/674
2.4
0.40
20.9
3icb
137/654
0.8
0.34
21.5
4pti
1/687
3.5
0.48
45.6
4rxn
83/677
1.1
0.31
19.4
fisa
1fc2
497/501
−2.2
−0.22
4.0
1hddC
442/501
−1.2
−0.02
8.0
2cro
32/501
1.5
0.07
10.0
4icb
465/500
−1.4
−0.02
6.0
fisa_casp3
1bg8A
10/1201
2.4
0.06
14.2
1bl0
883/972
−1.4
−0.19
5.2
1eh2
1624/2414
−0.5
0.09
16.2
1jwe
539/1408
0.3
0.04
9.3
smd3
1/1201
2.8
0.07
10.0
hg_structal
1ash
2/30
2.2
0.47
33.3
1babB
1/30
3.7
0.17
66.7
1colA
1/30
3.9
0.46
33.3
1cpcA
4/30
1.4
0.19
0.0
1ecd
11/30
0.3
0.00
0.0
1emy
1/30
3.3
0.38
66.7
1flp
1/30
2.3
0.21
66.7
1gdm
3/30
1.5
0.12
33.3
1hbg
1/30
2.8
0.03
33.3
1hbhA
1/30
3.4
0.18
33.3
1hbhB
3/30
1.7
−0.27
33.3
1hdaA
1/30
5.2
0.27
33.3
1hdaB
1/30
4.2
0.42
33.3
1hlb
1/30
2.0
0.25
33.3
1hlm
5/30
0.9
0.12
0.0
1hsy
12/30
0.3
0.49
33.3
1ithA
1/30
3.4
0.17
66.7
1lht
13/30
0.1
0.12
0.0
1mba
1/30
5.7
0.31
33.3
1mbs
30/30
−2.8
0.16
33.3
1mygA
3/30
1.3
0.25
66.7
1myjA
14/30
0.1
0.29
0.0
1myt
20/30
−0.8
0.06
33.3
2dhbA
30/30
−2.0
−0.23
33.3
2dhbB
24/30
−0.9
0.45
33.3
2lhb
1/30
4.7
0.49
66.7
2pghA
6/30
1.1
0.24
33.3
2pghB
1/30
2.7
0.29
33.3
4sdhA
1/30
2.7
−0.01
33.3
lattice_ssfit
1beo
1/1999
4.9
0.04
7.0
1ctf
88/2001
1.7
−0.04
11.0
1dktA
13/1999
2.5
0.00
8.5
1fca
3/2001
3.1
0.03
16.0
1nkl
92/1998
1.7
0.01
17.1
1pgb
506/2000
0.7
−0.04
13.0
1trlA
68/2000
1.8
0.03
10.5
4icb
223/2000
1.2
−0.03
13.0
ig_structal_hires
1dvf
1/20
2.1
0.13
50.0
1fgv
1/20
3.9
0.20
50.0
1flr
16/20
−0.3
−0.08
0.0
1fvc
1/20
3.5
0.56
50.0
1gaf
1/20
3.8
−0.01
50.0
1hil
1/20
2.6
0.55
50.0
1ind
7/20
0.2
0.36
0.0
1kem
1/20
2.4
0.46
50.0
1mfa
1/20
2.0
0.10
50.0
1mlb
9/20
0.2
−0.51
0.0
1nbv
11/20
−0.2
0.20
0.0
1opg
20/20
−3.8
−0.45
0.0
1vfa
1/20
2.2
0.39
50.0
1vge
2/20
1.9
0.42
50.0
2cgr
1/20
2.6
0.39
50.0
2fb4
7/20
0.3
−0.09
0.0
2fbj
19/20
−1.1
−0.12
0.0
6fab
3/20
1.5
0.25
0.0
7fab
10/20
0.2
0.27
0.0
8fab
1/20
2.6
0.14
50.0
ig_structal
1acy
56/61
−1.5
−0.01
0.0
1baf
3/61
2.1
0.12
16.7
1bbd
61/61
−3.1
−0.15
0.0
1bbj
23/61
0.1
−0.02
0.0
1dbb
24/61
0.1
−0.31
0.0
1dfb
8/61
1.1
0.20
0.0
1dvf
1/61
2.7
0.11
16.7
1eap
1/61
2.6
0.16
16.7
1fai
2/61
1.9
0.29
33.3
1fbi
12/61
0.8
−0.06
33.3
1fgv
1/61
2.9
0.03
16.7
1fig
2/61
2.0
0.11
16.7
1flr
40/61
−0.2
−0.08
16.7
1for
1/61
3.5
0.16
33.3
1fpt
1/61
3.7
0.12
16.7
1frg
4/61
1.5
0.39
16.7
1fvc
1/61
2.8
0.16
33.3
1fvd
9/61
1.1
0.09
33.3
1gaf
1/61
3.5
0.04
16.7
1ggi
9/61
1.1
−0.03
0.0
1gig
10/61
1.0
0.16
0.0
1hil
2/61
2.5
0.41
16.7
1hkl
1/61
4.3
0.01
16.7
1iai
1/61
3.0
0.15
33.3
1ibg
30/61
0.0
−0.08
16.7
1igc
55/61
−1.3
0.02
0.0
1igf
6/61
1.3
0.10
16.7
1igi
2/61
1.9
0.13
16.7
1igm
43/61
−0.5
0.09
0.0
1ikf
1/61
2.7
0.35
50.0
1ind
20/61
0.5
0.31
0.0
1jel
1/61
3.5
0.02
16.7
1jhl
1/61
3.1
0.16
33.3
1kem
1/61
2.8
0.26
33.3
1mam
1/61
2.0
0.31
33.3
1mcp
60/61
−1.8
0.23
0.0
1mfa
4/61
1.6
−0.01
16.7
1mlb
23/61
0.4
−0.19
0.0
1mrd
2/61
2.6
0.28
33.3
1nbv
36/61
−0.2
0.03
0.0
1ncb
12/61
0.9
−0.02
16.7
1ngq
13/61
0.8
0.00
0.0
1nmb
1/61
2.9
0.38
16.7
1nsn
8/61
1.0
−0.11
0.0
1opg
61/61
−2.7
−0.01
0.0
1plg
2/61
1.8
−0.02
16.7
1rmf
3/61
1.8
0.01
16.7
1tet
2/61
2.6
−0.15
16.7
1ucb
1/61
4.3
0.33
16.7
1vfa
1/61
2.5
0.20
16.7
1vge
3/61
2.1
0.03
16.7
1yuh
22/61
0.6
−0.02
16.7
2cgr
1/60
2.5
0.17
16.7
2fb4
19/61
0.4
−0.12
0.0
2fbj
53/61
−0.9
0.12
16.7
2gfb
1/61
2.9
0.28
16.7
3hfl
12/61
1.0
0.20
16.7
3hfm
61/61
−4.3
−0.16
0.0
6fab
7/61
1.4
0.02
0.0
7fab
23/61
0.3
0.01
0.0
8fab
1/61
3.1
0.04
16.7
lmds
1b0nB
1/498
3.9
0.05
10.2
1bba
496/501
−2.1
0.03
18.0
1ctf
32/498
1.6
0.03
14.3
1dtk
206/216
−1.7
0.04
14.3
1fc2
247/501
0.0
0.05
16.0
1igd
342/501
−0.4
0.14
10.0
1shfA
223/438
0.1
−0.01
4.7
2cro
2/501
2.3
0.22
14.0
2ovo
110/348
0.4
0.05
11.8
4pti
26/344
1.5
0.02
14.7
smd3
1/501
3.5
0.01
10.0
Native rank = (rank of native structure with given PDB ID)/(total number of decoys); a rank of 1 is optimal and means the calculated energy of the native structure is lower than that of all its decoys; = correlation coefficient; FE = fractional enrichment.
