Project name: NovoTIM13

Status: done

Started: 2026-03-07 01:35:51
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                                          (00:00:02)
[INFO]       CABS:     Running CABS flex simulation                                                (00:04:53)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:36:23)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:36:24)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:36:25)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:36:26)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:36:27)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:36:28)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:36:28)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:36:29)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:36:30)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:36:31)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:36:32)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:36:33)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:36:34)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:36:38)
[INFO]       Main:     Simulation completed successfully.                                          (00:36:39)
Show buried residues
Minimal score value
-3.8654
Maximal score value
0.0
Average score
-1.1688
Total score value
-216.2351
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 -1.2023
2 D A -2.1251
3 V A -1.7353
4 D A -2.7489
5 E A -2.7746
6 M A 0.0000
7 L A -2.1278
8 K A -2.5006
9 Q A 0.0000
10 V A 0.0000
11 E A -2.4569
12 I A -1.6797
13 L A 0.0000
14 R A -3.2725
15 R A -2.6678
16 L A -1.4101
17 G A -1.7850
18 A A -1.8309
19 K A -2.1446
20 Q A -1.4889
21 I A 0.0000
22 A A 0.0000
23 V A 0.0000
24 R A -0.6089
25 S A 0.0000
26 D A -1.6390
27 D A -1.3252
28 W A -1.2106
29 R A -1.8817
30 I A -1.2358
31 L A 0.0000
32 Q A -1.4030
33 E A -1.9044
34 A A 0.0000
35 L A -1.5716
36 K A -2.2598
37 K A -2.3715
38 G A -1.7835
39 G A 0.0000
40 D A -0.9813
41 I A 0.0000
42 L A 0.0000
43 I A 0.0000
44 V A 0.0000
45 D A -1.0472
46 A A -1.6525
47 T A -1.3955
48 D A -2.3113
49 V A -1.2547
50 D A -2.6166
51 E A -2.7066
52 M A 0.0000
53 L A 0.0000
54 K A -2.3486
55 Q A 0.0000
56 V A 0.0000
57 E A -2.1897
58 I A -1.2618
59 L A 0.0000
60 R A -1.9847
61 R A -1.9314
62 L A -0.5536
63 G A -1.1959
64 A A 0.0000
65 K A -1.9437
66 Q A -1.2070
67 I A 0.0000
68 A A 0.0000
69 V A 0.0000
70 R A -1.1286
71 S A -1.3117
72 D A -2.4666
73 D A -1.8979
74 W A -1.2948
75 R A -2.0755
76 I A -1.1938
77 L A 0.0000
78 Q A -1.5364
79 E A -2.0763
80 A A 0.0000
81 L A -1.6814
82 K A -2.5266
83 K A -2.4138
84 G A -1.8670
85 G A 0.0000
86 D A 0.0000
87 I A 0.0000
88 L A 0.0000
89 I A 0.0000
90 V A 0.0000
91 D A -1.4118
92 A A -1.9099
93 T A -1.7728
94 D A -2.7644
95 V A -2.6419
96 D A -3.4598
97 E A -3.8654
98 M A 0.0000
99 L A 0.0000
100 K A -3.0279
101 Q A 0.0000
102 V A 0.0000
103 E A -2.1800
104 I A -1.2595
105 L A 0.0000
106 R A -2.2227
107 R A -1.8643
108 L A -0.3242
109 G A -1.2726
110 A A 0.0000
111 K A -1.8945
112 Q A -1.2527
113 I A 0.0000
114 A A 0.0000
115 V A 0.0000
116 R A -1.0865
117 S A 0.0000
118 D A -2.4648
119 D A -2.0774
120 W A -1.6652
121 R A -2.2467
122 I A 0.0000
123 L A 0.0000
124 Q A -1.6408
125 E A -2.3054
126 A A 0.0000
127 L A -1.7128
128 K A -2.7958
129 K A -3.1751
130 G A -2.0121
131 G A 0.0000
132 D A -1.0432
133 I A 0.0000
134 L A 0.0000
135 I A 0.0000
136 V A 0.0000
137 D A -1.5857
138 A A -1.6067
139 T A -1.6964
140 D A -2.3109
141 V A -1.9217
142 D A -2.6756
143 E A -2.5073
144 M A 0.0000
145 L A -1.8657
146 K A -2.0233
147 Q A 0.0000
148 V A 0.0000
149 E A -2.0168
150 I A -1.2825
151 L A 0.0000
152 R A -2.0160
153 R A -1.9177
154 L A -0.5897
155 G A -1.4022
156 A A 0.0000
157 K A -1.9732
158 Q A -1.2927
159 I A 0.0000
160 A A 0.0000
161 V A 0.0000
162 R A 0.0000
163 S A 0.0000
164 D A -2.3896
165 D A -2.1739
166 W A -1.7331
167 R A -2.4761
168 I A -1.7515
169 L A 0.0000
170 Q A -1.4958
171 E A -1.9827
172 A A 0.0000
173 L A -1.3638
174 K A -2.3065
175 K A -1.9686
176 G A -1.4334
177 G A 0.0000
178 D A 0.0000
179 I A 0.0000
180 L A 0.0000
181 I A 0.0000
182 V A 0.0000
183 D A -1.1148
184 A A 0.0000
185 T A -0.8125
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, -1.1688 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
input -1.1688 View CSV PDB
model_1 -1.2155 View CSV PDB
model_0 -1.3256 View CSV PDB
model_7 -1.3286 View CSV PDB
model_5 -1.3625 View CSV PDB
CABS_average -1.4015 View CSV PDB
model_2 -1.402 View CSV PDB
model_10 -1.4126 View CSV PDB
model_4 -1.4152 View CSV PDB
model_3 -1.4209 View CSV PDB
model_9 -1.4694 View CSV PDB
model_6 -1.4834 View CSV PDB
model_11 -1.4898 View CSV PDB
model_8 -1.4926 View CSV PDB