Project name: D26G_dyn [mutate: DG26A]

Status: done

Started: 2025-05-05 23:13:28
Chain sequence(s) A: GTKITFYEDKNFQGRRYDCDCDCADFHTYLSRCNSIKVEGGTWAVYERPNFAGYMYILPQGEYPEYQRWMGLNDRLSSCRAVHLPSGGQYKIQIFEKGDFSGQMYETTEDCPSIMEQFHMREIHSCKVLEGVWIFYELPNYRGRQYLLDKKEYRKPIDWGAASPAVQSFRRIVE
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage Used: no changes made
Dynamic mode Yes
Automated mutations No
Mutated residues DG26A
Energy difference between WT (input) and mutated protein (by FoldX) 0.230728 kcal/mol
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       PDB:      Running AlphaCutter                                                         (00:00:01)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:07)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:07)
[INFO]       FoldX:    Building mutant model                                                       (00:03:41)
[INFO]       CABS:     Running CABS flex simulation                                                (00:03:49)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:33:14)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:33:14)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:33:15)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:33:16)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:33:16)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:33:17)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:33:18)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:33:19)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:33:19)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:33:20)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:33:21)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:33:21)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:33:22)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:33:27)
[INFO]       Main:     Simulation completed successfully.                                          (00:33:28)
Show buried residues
Minimal score value
-3.7814
Maximal score value
1.8586
Average score
-0.936
Total score value
-162.8657
Download the table (csv)

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan4D score mutation
5 G A -1.9833
6 T A 0.0000
7 K A -3.7814
8 I A 0.0000
9 T A -2.8721
10 F A 0.0000
11 Y A 0.0000
12 E A 0.0000
13 D A -2.7501
14 K A -2.8591
15 N A -2.2833
16 F A -1.1127
17 Q A -2.1342
18 G A -2.3062
19 R A -3.1952
20 R A -3.3362
21 Y A -1.7871
22 D A -3.0754
23 C A -2.3540
24 D A -3.0833
25 C A 0.0000
26 G A -1.6075 mutated: DG26A
27 C A -0.7130
28 A A -0.6367
29 D A -1.2508
30 F A 0.0000
31 H A -0.6799
32 T A 0.5752
33 Y A 1.5962
34 L A 1.8586
35 S A 0.3530
36 R A -0.8959
37 C A 0.0000
38 N A 0.0000
39 S A 0.0000
40 I A 0.0000
41 K A -3.2451
42 V A 0.0000
43 E A -3.3113
44 G A -2.4685
45 G A -1.5335
46 T A 0.0000
47 W A 0.0000
48 A A 0.0000
49 V A 0.0000
50 Y A -0.5106
51 E A 0.0000
52 R A -1.9135
53 P A -0.8678
54 N A -0.8656
55 F A 0.9404
56 A A 0.0072
57 G A -0.3473
58 Y A 0.0000
59 M A 0.0000
60 Y A 0.0000
61 I A -0.0889
62 L A 0.0000
63 P A -1.6470
64 Q A -2.1709
65 G A -2.2123
66 E A -3.0069
67 Y A 0.0000
68 P A -2.4296
69 E A -2.6728
70 Y A 0.0000
71 Q A -2.1281
72 R A -2.4622
73 W A -1.0107
74 M A -0.6883
75 G A -0.3102
76 L A 0.8421
77 N A -0.0240
78 D A -0.9320
79 R A 0.0000
80 L A 0.0000
81 S A 0.0000
82 S A -1.0156
83 C A 0.0000
84 R A -2.0660
85 A A -1.4722
86 V A -0.5789
87 H A -0.7077
88 L A 0.4707
89 P A -0.8243
90 S A -1.0757
91 G A -1.1062
92 G A -2.0909
93 Q A -2.4264
94 Y A 0.0000
95 K A -2.1190
96 I A 0.0000
97 Q A -1.0926
98 I A 0.0000
99 F A 0.0000
100 E A 0.0000
101 K A -2.7367
102 G A -1.7928
103 D A -2.1909
104 F A -0.7176
105 S A -0.5968
106 G A -0.9107
107 Q A -0.9760
108 M A 0.1041
109 Y A -0.3286
110 E A -1.7753
111 T A -1.7090
112 T A -2.2009
113 E A -2.6667
114 D A 0.0000
115 C A -1.0552
116 P A -0.3736
117 S A 0.2358
118 I A 1.2818
119 M A 0.7018
120 E A -0.9842
121 Q A -0.6075
122 F A -0.2733
123 H A -1.5421
124 M A -1.7259
125 R A -3.1950
126 E A -3.2863
127 I A 0.0000
128 H A -2.4657
129 S A 0.0000
130 C A 0.0000
131 K A -1.6535
132 V A 0.0000
133 L A -1.0731
134 E A -1.9178
135 G A -1.3236
136 V A 0.0000
137 W A 0.0000
138 I A 0.0000
139 F A 0.0000
140 Y A -0.3493
141 E A 0.0000
142 L A -0.5392
143 P A -0.8800
144 N A -1.0846
145 Y A -0.1681
146 R A -1.5185
147 G A 0.0000
148 R A -0.6157
149 Q A 0.0000
150 Y A 0.0000
151 L A -0.3611
152 L A 0.0000
153 D A -2.2552
154 K A -3.1103
155 K A -2.9501
156 E A -2.2791
157 Y A 0.0000
158 R A -2.1010
159 K A -2.2616
160 P A -0.7234
161 I A 1.1148
162 D A -0.6212
163 W A -0.4645
164 G A -0.7270
165 A A 0.0000
166 A A -1.2533
167 S A -0.6716
168 P A -0.9760
169 A A -1.2239
170 V A 0.0000
171 Q A -0.3621
172 S A 0.0637
173 F A 0.0000
174 R A -1.6309
175 R A -2.3604
176 I A -1.3749
177 V A 0.0000
178 E A -1.9493
Download PDB file
View in 3Dmol

CABS-flex predictions of flexibility of input structure

In dynamic mode, A4D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A4D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A4D score, -0.936 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A4D Score
model_3 -0.936 View CSV PDB
model_2 -0.9526 View CSV PDB
model_11 -0.9527 View CSV PDB
model_6 -0.9769 View CSV PDB
model_7 -0.9948 View CSV PDB
model_9 -1.0015 View CSV PDB
model_0 -1.007 View CSV PDB
CABS_average -1.0128 View CSV PDB
model_8 -1.0229 View CSV PDB
model_1 -1.033 View CSV PDB
model_4 -1.0511 View CSV PDB
model_5 -1.0608 View CSV PDB
input -1.0977 View CSV PDB
model_10 -1.1648 View CSV PDB