Project name: NovoTIM13

Status: done

Started: 2026-02-27 20:46:55
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]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       CABS:     Running CABS flex simulation                                                (00:04:27)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:46:18)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:46:19)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:46:20)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:46:21)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:46:23)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:46:24)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:46:25)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:46:26)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:46:28)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:46:29)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:46:30)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:46:31)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:46:33)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:46:39)
[INFO]       Main:     Simulation completed successfully.                                          (00:46:41)
Show buried residues
Minimal score value
-3.2844
Maximal score value
0.0
Average score
-1.1594
Total score value
-214.4919
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 -1.2731
2 D A -2.5393
3 V A -1.7576
4 D A -2.9612
5 E A -3.2844
6 M A 0.0000
7 L A -2.2803
8 K A -2.4934
9 Q A 0.0000
10 V A 0.0000
11 E A -1.7547
12 I A -1.1048
13 L A 0.0000
14 R A -1.8975
15 R A -1.9323
16 L A -1.1199
17 G A -1.5783
18 A A 0.0000
19 K A -1.9070
20 Q A -1.1386
21 I A 0.0000
22 A A 0.0000
23 V A 0.0000
24 R A -0.7737
25 S A 0.0000
26 D A -2.5238
27 D A -1.8327
28 W A -1.5432
29 R A -2.1941
30 I A -1.4212
31 L A 0.0000
32 Q A -1.6743
33 E A -2.1772
34 A A 0.0000
35 L A -1.7013
36 K A -2.4243
37 K A -2.2251
38 G A -1.2864
39 G A 0.0000
40 D A 0.0000
41 I A 0.0000
42 L A 0.0000
43 I A 0.0000
44 V A 0.0000
45 D A 0.0000
46 A A -1.5118
47 T A -1.5530
48 D A -2.5408
49 V A -1.7080
50 D A -2.9534
51 E A -3.0258
52 M A 0.0000
53 L A -2.4477
54 K A -2.6603
55 Q A 0.0000
56 V A 0.0000
57 E A -2.8444
58 I A -1.7208
59 L A 0.0000
60 R A -2.4328
61 R A -2.2837
62 L A -1.3131
63 G A -1.6192
64 A A 0.0000
65 K A -1.9181
66 Q A -1.1601
67 I A 0.0000
68 A A 0.0000
69 V A 0.0000
70 R A -0.7762
71 S A 0.0000
72 D A -2.5238
73 D A -1.8452
74 W A -1.5504
75 R A -2.1620
76 I A -1.5222
77 L A 0.0000
78 Q A -1.6404
79 E A -2.1450
80 A A 0.0000
81 L A -1.8289
82 K A -2.7355
83 K A -2.8446
84 G A -1.9570
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 0.0000
92 A A -1.5585
93 T A -1.5531
94 D A -2.4841
95 V A -1.6301
96 D A -2.9419
97 E A -3.1228
98 M A 0.0000
99 L A -2.2538
100 K A -2.4756
101 Q A 0.0000
102 V A 0.0000
103 E A -2.2807
104 I A -1.5155
105 L A 0.0000
106 R A -2.1992
107 R A -2.1374
108 L A -1.0025
109 G A -1.5929
110 A A 0.0000
111 K A -1.9237
112 Q A -1.1570
113 I A 0.0000
114 A A 0.0000
115 V A 0.0000
116 R A -1.0648
117 S A 0.0000
118 D A -2.4777
119 D A -1.8821
120 W A -1.4681
121 R A -2.0582
122 I A -1.4415
123 L A 0.0000
124 Q A -1.4008
125 E A -1.8326
126 A A 0.0000
127 L A -1.5963
128 K A -2.4381
129 K A -2.3064
130 G A -1.6465
131 G A 0.0000
132 D A 0.0000
133 I A 0.0000
134 L A 0.0000
135 I A 0.0000
136 V A 0.0000
137 D A -1.4509
138 A A -1.5748
139 T A -1.5561
140 D A -1.8448
141 V A -1.6898
142 D A -2.7918
143 E A -2.9941
144 M A 0.0000
145 L A -2.0168
146 K A -2.4175
147 Q A 0.0000
148 V A 0.0000
149 E A -1.6881
150 I A -1.0906
151 L A 0.0000
152 R A -2.1784
153 R A -1.9420
154 L A -0.7818
155 G A -1.4844
156 A A 0.0000
157 K A -1.9202
158 Q A -1.1594
159 I A 0.0000
160 A A 0.0000
161 V A 0.0000
162 R A -1.1142
163 S A 0.0000
164 D A -2.5073
165 D A -2.0386
166 W A -1.5844
167 R A -2.0002
168 I A -1.4981
169 L A 0.0000
170 Q A -1.3885
171 E A -1.7579
172 A A 0.0000
173 L A -1.6339
174 K A -2.2704
175 K A -2.2555
176 G A -1.5326
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 0.0000
184 A A 0.0000
185 T A -0.8630
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, -1.1594 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 -1.1594 View CSV PDB
model_0 -1.2286 View CSV PDB
model_6 -1.2735 View CSV PDB
model_3 -1.2814 View CSV PDB
model_2 -1.3031 View CSV PDB
model_4 -1.3214 View CSV PDB
model_8 -1.3271 View CSV PDB
model_11 -1.3286 View CSV PDB
CABS_average -1.3298 View CSV PDB
model_1 -1.3419 View CSV PDB
model_9 -1.3656 View CSV PDB
model_7 -1.3702 View CSV PDB
model_10 -1.407 View CSV PDB
model_5 -1.4092 View CSV PDB