Supplementary information for the manuscript:
A Robust Algorithm for Optimizing Protein
Structures with NMR Chemical Shifts
Mark Berjanskii1, David Arndt1, Yongjie Liang1, and David S. Wishart 1,2,3†
1
Department of Computing Science, University of Alberta; 2Department of Biological
Sciences, University of Alberta and 3National Research Council, National Institute for
Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8
† To whom correspondence should be addressed. (Phone: 780-492-0383, email:
david.wishart@ualberta.ca)
Keywords: protein, structure determination, NMR, chemical shifts
1
Supplementary Figure Legends.
Supplementary Figure 1. CONTRA MD biasing in CS-GAMDy. Each biased MD
iteration consists of 50 independent MD runs with different starting velocities and several
other starting MD parameters. At the end of each biased MD step, final models from
these 50 runs are assessed and ranked by the GeNMR knowledge-based function or the
RCI-ASA score. The best-scoring model becomes the starting model for the next round
of MD biasing.
Supplementary Figure 2. CS-GAMDy operation modes. (A) Default full mode: includes
both the genetic algorithm and biased molecular dynamics (MD). (B) Only the genetic
algorithm for MD without biasing. (C) Only biased MD (D) Only MD without biasing or
the genetic algorithm.
Supplementary Figure 3. CS-GAMDy stop criteria. (A) Changes in the GeNMR score
during CS-GAMDy refinement of a misfolded ubiquitin model. The end of the GeNMR
score decay (step 220) is labeled with a blue arrow. The termination point (220 X 5 = step
1100) is shown with a red arrow. (B) C RMSD to the reference model (1UBQ) during
the same CS-GAMDy refinement. The RMSD shows no significant changes between the
end of the GeNMR score decay (step 220) and the CS-GAMDy termination point (step
1100).
Supplementary Figure 4. CS-GAMDy success criteria. (A) GeNMR score vs C RMSD
to the best-scoring model. The score drop criterion, the RMSD criterion, and correlation
2
coefficient criterion are indicated with green, black, and red lines, respectively. See the
text for explanations of these simulation success criteria. (B) GeNMR score vs C
RMSD to the reference model (PDB ID: 1UBQ). The plot demonstrates a good
correlation between the GeNMR score and the model accuracy.
Supplementary Figure 5. Performance of CS-GAMDy for misfolded models of several
proteins from the CS-GAMDy testing set. Model accuracy (backbone RMSD of non-coil
regions with respect to the reference structure) is plotted on the X axis (before
refinement) and Y axis (after refinement), respectively.
3
Supplementary Figure 1.
4
Supplementary Figure 2.
5
Supplementary Figure 3
6
Supplementary Figure 4
7
Supplementary Figure 5.
8
Supplementary Table 1. Scores and energy terms that are used in CS-GAMDy.
Scores or
energies
ANGLes
BONDs
IMPRoper
DIHEdral
VDW
ELEC
RAMA
HBDB
RGYR
GBIN,
GBSE
CDIH
NOE
goap
RW
Hcount
HBener
Rama
Chi1
Omega
Bump
Rad
Thread
SecStr
N
CA
CO
CB
HA
HN
RCI-ASA
Optimization target
Program
Role in CS-GAMDy
Bond angles
Bond length
Planarity or chirality
Torsion angles
van der Waals interactions
Electrostatic interactions
Torsion angle normality
Hydrogen bonding
Radius of gyration
XPLOR
XPLOR
XPLOR
XPLOR
XPLOR
XPLOR
XPLOR
XPLOR
XPLOR
Molecular dynamics
Molecular dynamics
Molecular dynamics
Molecular dynamics
Molecular dynamics
Molecular dynamics
Molecular dynamics
Molecular dynamics
Molecular dynamics
Solvent properties
XPLOR
Molecular dynamics
XPLOR
Molecular dynamics
XPLOR
Molecular dynamics
GOAP
RW
GeNMR
GeNMR
GeNMR
GeNMR
GeNMR
GeNMR
GeNMR
Genetic algorithm
Genetic algorithm (GA)
MD biasing, GA
MD biasing, GA
MD biasing, GA
MD biasing, GA
MD biasing, GA
MD biasing, GA
MD biasing, GA
MD biasing, GA
GeNMR
MD biasing, GA
GeNMR
GeNMR
GeNMR
GeNMR
GeNMR
GeNMR
MD biasing, GA
MD biasing, GA
MD biasing, GA
MD biasing, GA
MD biasing, GA
MD biasing, GA
CSGAMDy
MD biasing, GA
Agreement with torsion angle
restraints
Agreement with distance
restraints
Pairwise atomic interactions
Intra-protein distances
Hydrogen bonding
Hydrogen bonding
Phi and Psi torsion angles
Side-chain torsion angles
Omega torsion angles
van der Waals interactions
Radius of gyration
Intramolecular interactions
Agreement with secondary
structure from chemical shifts
Agreement with 15N shifts
Agreement with 13C shifts
Agreement with 13CO shifts
Agreement with 13Cβ shifts
Agreement with 1H shifts
Agreement with 1HN shifts
Average of Pearson and
Kendall Tau coefficients of
correlation between RCIderived ASA and model ASA
9
Supplementary Table 2. Important parameters of molecular dynamics and minimization
in CS-GAMDy
Parameter
Temperature
Force-field
Coefficient for
dihedral angle
restraints
Time step
MD length
MD
minimization
Minimization
steps
Description
MD virtual temperature.
Ignored if temperature
randomization during
GA is activated.
MD force-field. Forcefield files are stored in
Python dictionary
“ff_dict” and include
PARALLHDG, OPLS.
CHARMM, and Amber
Weighting coefficient
for dihedral angle
restraints. Ignored if its
randomization during
MD biasing is selected.
MD integration time
step. Ignored if its
randomization during
MD biasing is selected
Number of MD steps
If 1, quench MD with
Powell’s minimization.
Number of Powell’s
minimization steps.
XPLOR will stop
minimization faster if
model changes get too
small
Parameter
flag
-temp
-ff
Default value
40,000K
parallhdg_new,
which corresponds
to force-field file
parallhdg_new.pro
-cdih_coef
200
-timestep
0.002 ps
-md_length
10
-post_min
1
-post_min_steps
1000
10
Supplementary Table 3. Important parameters of MD biasing (BMD) in CS-GAMDy
Parameter
Temperature
randomization in
MD biasing
Description
If 1, use temperature that is
randomly selected between 10K
and the maximal temperature
defined either with “-temp” (vide
supra) or “-ga_temp_random”
(vide infra) flags.
Random radius If 1, randomly select weight for
of gyration
the radius of gyration term from
weight
the range between 1 and 500.
Random weight
If 1, randomly select weight for
of van der Waals
the van der Waals interactions
interactions
term from between 0 and 1
Random weight
If 1, randomly select weight for
of the
the electrostatic interactions term
electrostatic term
from between 0 and 1
Random weight
Key in Python dictionary
of the torsion
“cdih_coef_range” that stores
angle restraints
weights for torsion angle
restraints. Default key 9
corresponds to the set: 0, 2000 If
0, no randomization is done
Time step
If 1, use time step randomly
randomization in
selected between 0.00001ps and
MD biasing
the maximal time step.
Maximal time
Maximal time step in time step
step
randomization
MD length
If 1, use MD length that is
randomization in randomly selected between 1 and
MD biasing
the maximal MD length.
Maximal MD
Maximal length in MD length
length
randomization
Number of
Number of independent MD
independent MD trajectories starting from the same
trajectories
model.
BMD length
Number of BMD iterations
BMD ASA score
This parameter enables optional
model ranking by an accessible
surface area (ASA) score.
Available scores are pearson,
kendall, and pearken (mean of
pearson and kendall correlation
coefficients )
Parameter
flag
Default
value
-bmd_temp_random
1
-rgyr_random
1
-vdw_random
1
-elec_random
1
-cdih_random
9
-bmd_ts_random
1
-max_timestep
-bmd_mdl_random
0.01 ps
1
-max_mdl
100
-ns
50
-bmd_length
10
-bmd_asa
pearken
11
Supplementary Table 4. Important parameters of genetic algorithm in CS-GAMDy
Parameter
Description
Parameter
flag
Default value
Key in Python dictionary
“ga_temp_range_dict” that
stores sets of randomly
Temperature
selected temperatures. If 0,
randomization
no randomization is done
-ga_temp_random 9
in genetic
Default key 9 corresponds to
algorithm
the set: 10,000, 20,000,
40,000, 80,000, 160,000,
320,000, 600,000, 1,000,000.
Number of MD biasing
Population
-pop
10
trajectories in GA population
Number of MD biasing
Number of
trajectories with least-fit
-nlos
2
losers
final models that get replaced
with the best-fit model
Types of fitness functions
that are being randomly
used. There are currently two
types of functions:
“GNMR_combo” and
scoring,
GA scores
“scoring”. Ranking function
-ga_score
GNMR_combo
“scoring” enables selection
of GOAP, RW, and ASA
scores. “GNMR_combo”
function ranks models with
GeNMR score
This parameter enables
GA GOAP
optional model ranking by
-ga_goap
total_goap_score
score
the GOAP score
This parameter enables
GA RW score
optional model ranking by
-ga_rw
rw
the RW score
This parameter enables
optional model ranking by an
accessible surface area
GA ASA
(ASA) score. Available
-ga_asa
pearken
score
scores are pearson, kendall,
and pearken (mean of
pearson and kendall
correlation coefficients )
12
Supplementary Table 5. Information on the distorted protein models.
Protein name
PyJ
Ubiquitin
GB3
Q5E7H1
RPA3401
RHOS4
26430
Protein LX
PefI
tRNA
hydrolase
domain
CSPA
Calbindin
D9K
NE1242
PDB ID
BMRB ID
Length
Folding class
1FAF
1UBQ
1P7E
2JVW
2JTV
4403
5387
18531
15491
15419
79
76
56
88
65

/β
/β

/β
2JVM
15482
80
β
2JXT
2JT1
15573
15386
86
77
/β
/β
2JVA
15471
108
/β
1MJC
4296
69
β
3ICB
19370
75

2JV8
15468
73
/β
13
Supplementary Table 6. Violations of dihedral angle restraints derived from NMR
chemical shifts by distorted protein models under different refinement scenarios.
Protein
name
PDB
ID
PyJ
Ubiquitin
GB3
Q5E7H1
RPA3401
RHOS4
26430
Protein
LX
PefI
tRNA
hydrolase
domain
CSPA
Calbindin
D9K
NE1242
Average
1FAF
1UBQ
1P7E
2JVW
2JTV
Violations of dihedral angle restraints derived from NMR
chemical shifts
Initial
Native
Refined
Refined
Refined by
model
by
by
CSXPLOR
CSGAMDy
with NMR GAMDy
with
data
without
NMR
NMR data
data
111
52
30
44
19
93
0
26
3
15
81
0
27
8
15
101
40
20
33
9
77
33
48
21
3
2JVM
55
29
0
39
15
2JXT
113
46
0
41
21
2JT1
93
37
57
36
0
2JVA
113
50
0
67
15
1MJC
84
17
5
74
3
3ICB
103
37
11
34
16
2JV8
85
92
51
35
15
15
43
40
2
10
14
Supplementary Table 7. Mean Pearson coefficient of correlation between experimental
and predicted backbone NMR chemical shifts of distorted protein models under different
refinement scenarios.
Protein
name
PDB
ID
PyJ
Ubiquitin
GB3
Q5E7H1
RPA3401
RHOS4
26430
Protein
LX
PefI
tRNA
hydrolase
domain
CSPA
Calbindin
D9K
NE1242
Average
1FAF
1UBQ
1P7E
2JVW
2JTV
Pearson coefficient of correlation between experimental and
predicted backbone NMR chemical shifts
Initial
Native
Refined by
Refined by
Refined by
model
XPLOR
CSCS-GAMDy
with NMR
GAMDy
with
data
without
NMR
NMR data
data
0.33
0.68
0.53
0.55
0.70
0.48
0.84
0.74
0.78
0.82
0.33
0.72
0.53
0.66
0.70
0.26
0.66
0.43
0.43
0.58
0.32
0.77
0.62
0.74
0.81
2JVM
0.29
0.64
0.55
0.46
0.59
2JXT
0.34
0.69
0.62
0.64
0.70
2JT1
0.34
0.81
0.62
0.68
0.80
2JVA
0.40
0.72
0.68
0.52
0.74
1MJC
0.36
0.78
0.55
0.38
0.79
3ICB
0.36
0.68
0.59
0.52
0.65
2JV8
0.41
0.35
0.63
0.72
0.68
0.59
0.58
0.58
0.73
0.72
15
Supplementary Table 8. Secondary structure score from NMR chemical shifts of distorted
protein models under different refinement scenarios. Note that a low score is good.
Protein
name
PyJ
Ubiquitin
GB3
Q5E7H1
RPA3401
RHOS4
26430
Protein
LX
PefI
tRNA
hydrolase
domain
CSPA
Calbindin
D9K
NE1242
Average
PDB
ID
GeNMR secondary structure score from NMR chemical shifts
Initial
model
Native
Refined
by
XPLOR
with NMR
data
Refined by
CSGAMDy
without
NMR data
1FAF
1UBQ
1P7E
2JVW
2JTV
184
160
148
196
188
20
28
20
20
32
36
44
104
32
52
44
56
16
40
36
Refined by
CSGAMDy
with
NMR
data
36
32
12
28
28
2JVM
96
48
92
64
32
2JXT
212
28
28
32
16
2JT1
180
28
40
52
20
2JVA
204
52
120
100
52
1MJC
116
28
128
92
24
3ICB
200
24
48
40
28
2JV8
164
171
68
33
120
70
72
54
28
28
16
Supplementary Table 9. Mean Pearson coefficient of correlation between model perresidue ASA and per-residue ASA predicted from NMR chemical shifts of distorted
protein models.
Protein
name
PDB
ID
PyJ
Ubiquitin
GB3
Q5E7H1
RPA3401
RHOS4
26430
Protein
LX
PefI
tRNA
hydrolase
domain
CSPA
Calbindin
D9K
NE1242
Average
1FAF
1UBQ
1P7E
2JVW
2JTV
Pearson coefficient of correlation between model’s ASA
and ASA predicted from chemical shifts
Initial Native Refined by
Refined
Refined by
model
XPLOR
by
CS-GAMDy
with NMR
CSwith
data
GAMDy
NMR
without
data
NMR data
0.28
0.81
0.31
0.65
0.73
0.50
0.65
0.41
0.63
0.58
0.58
0.55
0.45
0.54
0.61
0.31
0.77
0.12
0.72
0.70
0.51
0.65
0.31
0.63
0.54
2JVM
0.51
0.73
0.01
0.77
0.72
2JXT
0.35
0.49
0.33
0.51
0.49
2JT1
0.31
0.64
0.38
0.62
0.62
2JVA
0.30
0.58
0.21
0.56
0.46
1MJC
0.34
0.71
0.27
0.68
0.68
3ICB
0.56
0.12
0.46
0.10
0.34
2JV8
0.40
0.41
0.58
0.61
0.21
0.29
0.57
0.58
0.54
0.58
17
Supplementary Table 10. Violations of dihedral angle restraints derived from NMR
chemical shifts by ubiquitin comparative models under different refinement scenarios.
Template
PDB ID
ID
%
1OTR
2GBK
1UD7
2GBJ
2GBM
1WY8
2DZI
2FAZ
1OQY
1WH3
1WX9
1Z2M
1MG8
1UEL
1IYF
1WE7
1TTN
Average
96
92
91
90
90
39
39
37
36
36
34
33
32
32
30
28
26
Violations of dihedral angle restraints derived from NMR
chemical shifts
Initial
Refined by
Refined by
Refined by
model
XPLOR
CS-GAMDy CS-GAMDy
with NMR
without
with NMR
data
NMR data
data
62
1
34
1
25
1
39
0
44
1
36
0
23
0
41
3
27
3
26
2
74
118
55
2
67
1
41
1
38
83
43
7
89
16
47
3
74
0
34
0
78
0
33
5
35
0
33
6
72
2
38
13
63
1
46
2
75
1
46
0
89
2
53
0
89
33
74
0
60.2
15.5
42.3
2.7
18
Supplementary Table 11. Mean Pearson coefficient of correlation between experimental
and predicted backbone NMR chemical shifts of ubiquitin comparative models under
different refinement scenarios.
Template
PDB ID
ID
%
1OTR
2GBK
1UD7
2GBJ
2GBM
1WY8
2DZI
2FAZ
1OQY
1WH3
1WX9
1Z2M
1MG8
1UEL
1IYF
1WE7
1TTN
Average
96
92
91
90
90
39
39
37
36
36
34
33
32
32
30
28
26
Pearson coefficient of correlation between experimental and
predicted backbone NMR chemical shifts
Initial
Refined by
Refined by
Refined by
model
XPLOR with
CS-GAMDy
CS-GAMDy
NMR data
without NMR with NMR data
data
0.52
0.75
0.73
0.78
0.72
0.73
0.69
0.80
0.66
0.73
0.72
0.79
0.72
0.71
0.72
0.82
0.79
0.76
0.78
0.81
0.54
0.10
0.62
0.81
0.61
0.73
0.72
0.78
0.70
0.36
0.67
0.79
0.43
0.71
0.66
0.81
0.62
0.77
0.74
0.78
0.59
0.77
0.73
0.80
0.73
0.77
0.74
0.79
0.56
0.76
0.74
0.76
0.62
0.72
0.71
0.78
0.48
0.70
0.71
0.80
0.43
0.72
0.63
0.80
0.48
0.62
0.55
0.78
0.60
0.67
0.70
0.79
19
Supplementary Table 12. Secondary structure score from NMR chemical shifts of
ubiquitin comparative models under different refinement scenarios. Note that a low score
is good.
Template
PDB ID
ID
%
1OTR
2GBK
1UD7
2GBJ
2GBM
1WY8
2DZI
2FAZ
1OQY
1WH3
1WX9
1Z2M
1MG8
1UEL
1IYF
1WE7
1TTN
Average
96
92
91
90
90
39
39
37
36
36
34
33
32
32
30
28
26
GeNMR secondary structure score from NMR chemical
shifts
Initial
Refined by
Refined by
Refined by
model
XPLOR
CS-GAMDy
CS-GAMDy
with NMR
without
with NMR data
data
NMR data
48
72
44
40
72
108
76
28
68
48
56
32
88
72
48
32
48
32
32
24
96
160
72
32
44
88
32
32
104
160
48
28
88
76
40
32
40
44
44
28
52
44
32
32
52
44
40
28
60
44
36
28
24
96
36
28
68
56
36
28
72
72
52
28
60
96
48
28
63.8
77.2
45.4
29.9
20
Supplementary Table 13. Mean Pearson coefficient of correlation between model’s perresidue ASA and per-residue ASA predicted from backbone NMR chemical shifts of
ubiquitin comparative models under different refinement scenarios.
Template
PDB ID
ID
%
1OTR
2GBK
1UD7
2GBJ
2GBM
1WY8
2DZI
2FAZ
1OQY
1WH3
1WX9
1Z2M
1MG8
1UEL
1IYF
1WE7
1TTN
Average
96
92
91
90
90
39
39
37
36
36
34
33
32
32
30
28
26
Pearson coefficient of correlation between model’s ASA and
ASA predicted from chemical shifts
Initial model
Refined by
Refined by
Refined by
XPLOR with CS-GAMDy CS-GAMDy
NMR data
without
with NMR
NMR data
data
0.58
0.41
0.61
0.57
0.31
0.04
0.39
0.61
0.54
0.54
0.57
0.63
0.42
0.16
0.38
0.57
0.62
0.42
0.63
0.53
0.42
0.08
0.42
0.63
0.48
0.16
0.57
0.59
0.42
0.25
0.53
0.60
0.38
0.25
0.44
0.59
0.57
0.51
0.61
0.61
0.63
0.50
0.60
0.62
0.58
0.50
0.63
0.61
0.62
0.01
0.62
0.66
0.49
0.17
0.62
0.59
0.43
0.15
0.41
0.61
0.57
0.06
0.59
0.63
0.55
0.51
0.55
0.55
0.51
0.28
0.54
0.60
21
Supplementary Table 14. Comparative models with different sizes and types of protein
architecture along with the % identity to the comparative model template.
Protein
name
PyJ
Elongation
Factor 1
GB3
Foxo4
Hamster
PrP
Vts1
NifU-like
protein
cg2496
Cadherin
Adenylate
kinase
NFU1
homolog
Size
Folding
class
ID
% to
Template
4403
79

34
1F60
4117
91
/β
55
1P7E
1E17
1ZXH
2C6Y
18531
4675
56
150
/β
/β
63
42
1B10
1XYX
4307
142
/β
95
2D3D
2FE9
6922
88

96
2LTL
2FFM
18487
119
/β
19
2KPT
1SUH
2KW7
1EDH
16569
4380
148
146
/β
β
24
64
2CDN
1S3G
4840
201
/β
37
2M5O
1TH5
19068
97
/β
20
PDB ID
Template
PDB ID
BMRB
ID
1FAF
1GH6
1B64
22
Supplementary Table 15. Violations of dihedral angle restraints derived from NMR
chemical shifts that were observed in comparative models with different sizes and types
after their refinement under different refinement scenarios.
Protein
name
PDB
ID
PyJ
Elongation
Factor 1
GB3
Foxo4
Hamster PrP
Vts1
NifU-like
protein
cg2496
Cadherin
Adenylate
kinase
NFU1
homolog
Average
1FAF
Violations of dihedral angle restraints derived from
NMR chemical shifts
Initial Native Refined
Refined
Refined
model
by
by
by
XPLOR GAMDy
GAMDy
with
without
with
NMR
NMR
NMR
data
data
data
81
52
0
36
21
1B64
31
89
0
37
3
1P7E
1E17
1B10
2D3D
52
52
78
59
0
19
0
0
1
109
3
0
37
41
45
23
4
11
40
5
2LTL
81
61
22
85
10
2KPT
1SUH
78
49
120
69
39
1
64
52
1
15
2CDN
113
181
147
76
12
2M5O
79
37
8
69
5
68.5
58.2
30.0
51.4
11.5
23
Supplementary Table 16. Mean Pearson coefficient of correlation between experimental
and predicted backbone NMR chemical shifts of comparative models with different sizes
and types of protein architecture under different refinement scenarios.
Protein
name
PDB
ID
PyJ
Elongation
Factor 1
GB3
Foxo4
Hamster
PrP
Vts1
NifU-like
protein
cg2496
Cadherin
Adenylate
kinase
NFU1
homolog
Average
1FAF
Pearson coefficient of correlation between experimental
and predicted backbone NMR chemical shifts
Initial Native
Refined
Refined
Refined
model
by
by
by
XPLOR
GAMDy
GAMDy
with NMR
without
with
data
NMR data
NMR
data
0.50
0.68
0.59
0.54
0.69
1B64
0.79
0.67
0.74
0.75
0.78
1P7E
1E17
0.43
0.58
0.72
0.71
0.55
0.28
0.54
0.61
0.67
0.70
1B10
0.38
0.50
0.46
0.43
0.42
2D3D
0.60
0.77
0.61
0.70
0.67
2LTL
0.43
0.65
0.55
0.41
0.64
2KPT
1SUH
0.55
0.76
0.79
0.62
0.61
0.66
0.61
0.68
0.74
0.71
2CDN
0.56
0.66
0.37
0.61
0.63
2M5O
0.52
0.81
0.66
0.56
0.81
0.55
0.69
0.55
0.58
0.68
24
Supplementary Table 17. GeNMR secondary structure score from NMR chemical shifts
of comparative models with different sizes and types of protein architecture under
different refinement scenarios. Note that a low score is good.
Protein
name
PDB
ID
PyJ
Elongation
Factor 1
GB3
Foxo4
Hamster
PrP
Vts1
NifU-like
protein
cg2496
Cadherin
Adenylate
kinase
NFU1
homolog
Average
1FAF
GeNMR secondary structure score from NMR chemical
shifts
Initial Native Refined
Refined
Refined
model
by
by
by
XPLOR GAMDy
GAMDy
with
without
with
NMR
NMR
NMR
data
data
data
48
20
28
60
24
1B64
44
60
44
64
36
1P7E
1E17
60
64
20
40
56
156
36
56
20
56
1B10
40
28
44
56
24
2D3D
36
52
20
48
24
2LTL
124
48
92
132
52
2KPT
1SUH
144
100
60
92
128
92
156
84
80
88
2CDN
124
104
252
116
116
2M5O
100
32
76
100
68
80.4
52.0
89.8
82.5
53.5
25
Supplementary Table 18. Mean Pearson coefficient of correlation between model’s perresidue ASA and per-residue ASA predicted from backbone NMR chemical shifts of
comparative models with different sizes and types of protein architecture under different
refinement scenarios.
Protein
name
PDB
ID
PyJ
Elongation
Factor 1
GB3
Foxo4
Hamster
PrP
Vts1
NifU-like
protein
cg2496
Cadherin
Adenylate
kinase
NFU1
homolog
Average
1FAF
Pearson coefficient of correlation between model’s ASA
and ASA predicted from chemical shifts
Initial Native
Refined
Refined
Refined
model
by
by
by
XPLOR
GAMDy
GAMDy
with NMR
without
with
data
NMR data
NMR
data
0.70
0.81
0.58
0.59
0.57
1B64
0.64
0.64
0.54
0.58
0.55
1P7E
1E17
0.45
0.61
0.55
0.72
0.48
0.20
0.50
0.48
0.51
0.54
1B10
0.63
0.73
0.53
0.59
0.63
2D3D
0.55
0.59
0.46
0.50
0.50
2LTL
0.43
0.55
0.21
0.36
0.45
2KPT
1SUH
0.48
0.60
0.75
0.58
0.27
0.54
0.48
0.60
0.56
0.58
2CDN
0.56
0.62
0.22
0.50
0.54
2M5O
0.57
0.64
0.27
0.49
0.66
0.57
0.65
0.39
0.52
0.55
26