Project name: NovoTIM13

Status: done

Started: 2026-03-04 14:38:39
Chain sequence(s) A: MDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDILIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDILIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDILIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDILIVDAT
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
Dynamic mode Yes
Automated mutations No
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]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:06:07)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:37:39)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:37:40)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:37:41)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:37:41)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:37:42)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:37:43)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:37:44)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:37:45)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:37:45)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:37:46)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:37:47)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:37:48)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:37:49)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:37:53)
[INFO]       Main:     Simulation completed successfully.                                          (00:37:54)
Show buried residues
Minimal score value
-3.9069
Maximal score value
0.2708
Average score
-1.2548
Total score value
-232.1368
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
1 M A -0.0722
2 D A -0.9684
3 V A 0.2708
4 D A -1.4924
5 E A -1.0435
6 M A -0.2988
7 L A -0.6497
8 K A -1.3183
9 Q A 0.0000
10 V A 0.0000
11 E A -1.7789
12 I A -0.7404
13 L A 0.0000
14 R A -2.3380
15 R A -1.9742
16 L A -0.7556
17 G A -1.4874
18 A A 0.0000
19 K A -1.8298
20 Q A -1.3805
21 I A 0.0000
22 A A 0.0000
23 V A 0.0000
24 R A 0.0000
25 S A 0.0000
26 D A -1.7330
27 D A -2.2438
28 W A -1.9140
29 R A -2.4601
30 I A -1.2291
31 L A 0.0000
32 Q A -1.8299
33 E A -1.6491
34 A A 0.0000
35 L A -1.2870
36 K A -2.1713
37 K A -1.9811
38 G A -1.5312
39 G A 0.0000
40 D A -1.1227
41 I A -0.5789
42 L A 0.0000
43 I A 0.0000
44 V A 0.0000
45 D A 0.0000
46 A A -1.1568
47 T A -1.3178
48 D A -1.8876
49 V A -1.5743
50 D A -2.8844
51 E A -2.8820
52 M A 0.0000
53 L A -2.0273
54 K A -2.9514
55 Q A 0.0000
56 V A 0.0000
57 E A -2.6792
58 I A -1.5717
59 L A 0.0000
60 R A -3.2706
61 R A -2.6153
62 L A -1.4909
63 G A -1.4402
64 A A -1.6778
65 K A -2.2246
66 Q A -1.4368
67 I A 0.0000
68 A A 0.0000
69 V A 0.0000
70 R A -0.9562
71 S A 0.0000
72 D A -2.9992
73 D A -3.9069
74 W A 0.0000
75 R A -3.0140
76 I A -2.3597
77 L A 0.0000
78 Q A -2.4328
79 E A -2.4380
80 A A 0.0000
81 L A -1.7844
82 K A -2.2037
83 K A -2.2590
84 G A -1.7333
85 G A 0.0000
86 D A -1.4242
87 I A -0.7593
88 L A 0.0000
89 I A 0.0000
90 V A 0.0000
91 D A -1.5794
92 A A -1.5853
93 T A -1.6664
94 D A -2.1626
95 V A -2.2314
96 D A -3.3970
97 E A -3.8707
98 M A 0.0000
99 L A -2.6713
100 K A -3.3760
101 Q A -3.0798
102 V A 0.0000
103 E A -3.0113
104 I A -2.0232
105 L A -1.8423
106 R A -2.6225
107 R A -2.0950
108 L A -0.5014
109 G A -1.1783
110 A A -1.4215
111 K A -1.8502
112 Q A -1.5900
113 I A 0.0000
114 A A 0.0000
115 V A 0.0000
116 R A -0.9187
117 S A 0.0000
118 D A -2.7261
119 D A -2.5814
120 W A -1.7146
121 R A -2.5804
122 I A 0.0000
123 L A 0.0000
124 Q A -2.2298
125 E A -2.6600
126 A A 0.0000
127 L A -2.2417
128 K A -2.9921
129 K A -2.8850
130 G A -2.1945
131 G A 0.0000
132 D A -1.6405
133 I A 0.0000
134 L A 0.0000
135 I A 0.0000
136 V A 0.0000
137 D A -1.5190
138 A A -1.7222
139 T A -1.9607
140 D A -2.9114
141 V A -2.2768
142 D A -2.8314
143 E A -2.9285
144 M A 0.0000
145 L A -1.6312
146 K A -2.0980
147 Q A 0.0000
148 V A 0.0000
149 E A -2.4269
150 I A -1.6149
151 L A 0.0000
152 R A -3.2388
153 R A -2.7522
154 L A -1.5080
155 G A -1.5277
156 A A -1.7111
157 K A -1.8667
158 Q A -1.5705
159 I A -1.2080
160 A A 0.0000
161 V A 0.0000
162 R A 0.0000
163 S A 0.0000
164 D A -2.0051
165 D A -1.8879
166 W A -1.1484
167 R A -2.5075
168 I A 0.0000
169 L A 0.0000
170 Q A -1.6026
171 E A -2.5374
172 A A 0.0000
173 L A 0.0000
174 K A -2.2167
175 K A -1.7474
176 G A 0.0000
177 G A 0.0000
178 D A -1.7231
179 I A -0.7767
180 L A 0.0000
181 I A 0.0000
182 V A 0.0000
183 D A 0.0000
184 A A -0.3076
185 T A -0.3041
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, -1.2548 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 -1.2548 View CSV PDB
model_4 -1.2669 View CSV PDB
model_8 -1.2834 View CSV PDB
model_9 -1.2873 View CSV PDB
model_0 -1.2981 View CSV PDB
input -1.3043 View CSV PDB
CABS_average -1.3337 View CSV PDB
model_5 -1.3354 View CSV PDB
model_6 -1.3373 View CSV PDB
model_11 -1.3426 View CSV PDB
model_1 -1.3447 View CSV PDB
model_7 -1.3691 View CSV PDB
model_2 -1.3832 View CSV PDB
model_10 -1.5019 View CSV PDB