Project name: TIPM3_5_4D

Status: done

Started: 2026-05-22 05:08:06
Chain sequence(s) A: MTPWLGLIVLLGSWSLGDWGAEACTCSPSHPQDAFCNSDIVIRAKVVGKKLVKEGPFGTLVYTIKQMKMYRGFTKMPHVQYIHTEASESLCGLKLEVNKYQYLLTGRVYDGKMYTGLCNFVERWDQLTLSQRKGLNYRYHLGCNCKIKSCYYLPCFVTSKNECLWTDMLSNFGYPGYQSKHYACIRQKGGYCSWYRGWAPPDKSIINATDP
input PDB
Selected Chain(s) A
Distance of aggregation 5 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]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:00)
[INFO]       CABS:     Running CABS flex simulation                                                (00:03:01)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:30:43)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:30:44)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:30:45)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:30:45)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:30:46)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:30:47)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:30:47)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:30:48)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:30:49)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:30:50)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:30:50)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:30:51)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:30:52)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:30:55)
[INFO]       Main:     Simulation completed successfully.                                          (00:30:56)
Show buried residues
Minimal score value
-2.0161
Maximal score value
2.4241
Average score
-0.0365
Total score value
-7.7112
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 1.0193
2 T A 0.0901
3 P A 0.0681
4 W A 1.4264
5 L A 1.6805
6 G A 0.0209
7 L A 1.3472
8 I A 2.4241
9 V A 1.7963
10 L A 1.9436
11 L A 1.1462
12 G A -0.3250
13 S A -0.1039
14 W A 0.9643
15 S A 0.2986
16 L A 1.4416
17 G A -0.3345
18 D A -1.3142
19 W A 0.7190
20 G A 0.1356
21 A A -0.0578
22 E A -0.3145
23 A A 0.0000
24 C A 0.0000
25 T A -0.0085
26 C A 0.0551
27 S A -0.1910
28 P A 0.0000
29 S A -0.0254
30 H A 0.0000
31 P A -0.0277
32 Q A 0.0000
33 D A -0.7765
34 A A -0.2811
35 F A 0.0000
36 C A -0.0029
37 N A -1.2447
38 S A -0.4076
39 D A 0.0000
40 I A 0.4981
41 V A 0.0000
42 I A 0.0000
43 R A 0.0000
44 A A 0.0000
45 K A -0.9064
46 V A 0.3951
47 V A 1.7403
48 G A -0.2759
49 K A -1.4354
50 K A -1.7458
51 L A 0.6174
52 V A 0.6431
53 K A -1.7291
54 E A -1.3575
55 G A -0.6556
56 P A -0.1038
57 F A 0.2034
58 G A -0.2406
59 T A 0.0000
60 L A 0.0000
61 V A 0.2893
62 Y A 0.0000
63 T A 0.1973
64 I A 0.0000
65 K A -1.4187
66 Q A 0.0000
67 M A 0.2549
68 K A -0.2336
69 M A 0.1670
70 Y A 0.0280
71 R A -1.2718
72 G A -0.4500
73 F A 0.6828
74 T A -0.2225
75 K A -1.5111
76 M A 0.6667
77 P A -0.1032
78 H A -0.4552
79 V A 1.3081
80 Q A 0.4664
81 Y A 1.2892
82 I A 0.0000
83 H A -0.1409
84 T A 0.0000
85 E A 0.0000
86 A A -0.0365
87 S A -0.4504
88 E A -1.3517
89 S A -0.3969
90 L A 0.2965
91 C A 0.0670
92 G A -0.4200
93 L A -0.2482
94 K A -1.6328
95 L A -0.4823
96 E A -1.7846
97 V A 0.0000
98 N A -1.6028
99 K A -1.9195
100 Y A -0.2240
101 Q A 0.0000
102 Y A 0.0000
103 L A 0.0000
104 L A 0.0000
105 T A 0.0000
106 G A -0.1572
107 R A -0.2083
108 V A 1.9060
109 Y A 1.0148
110 D A -1.6759
111 G A -0.8900
112 K A -0.3566
113 M A 0.4509
114 Y A 0.1783
115 T A 0.0000
116 G A 0.0000
117 L A 0.0000
118 C A 0.0000
119 N A -0.1108
120 F A 0.0000
121 V A 0.2385
122 E A 0.0000
123 R A -1.4972
124 W A 0.0000
125 D A -0.4285
126 Q A -0.5091
127 L A 0.0000
128 T A 0.0000
129 L A 0.2725
130 S A -0.0442
131 Q A 0.0000
132 R A -0.3906
133 K A -0.7099
134 G A -0.2459
135 L A 0.0000
136 N A -0.1546
137 Y A 1.0499
138 R A -0.1661
139 Y A 0.0000
140 H A -0.0676
141 L A 1.4779
142 G A 0.0000
143 C A 0.5988
144 N A -0.1933
145 C A 0.0000
146 K A -1.0917
147 I A 0.0000
148 K A -1.7062
149 S A -0.1438
150 C A 0.4604
151 Y A 1.6021
152 Y A 1.8542
153 L A 1.7829
154 P A 0.6761
155 C A 1.0569
156 F A 2.0019
157 V A 0.6200
158 T A -0.0462
159 S A -0.5569
160 K A -1.8631
161 N A -1.1058
162 E A -0.5889
163 C A 0.0749
164 L A 0.3714
165 W A 0.0000
166 T A 0.0000
167 D A 0.0000
168 M A 0.4011
169 L A 0.0000
170 S A -0.4483
171 N A -1.1646
172 F A 0.4406
173 G A -0.2753
174 Y A 0.1230
175 P A -0.0927
176 G A 0.0668
177 Y A 0.9909
178 Q A -0.1611
179 S A 0.0000
180 K A -0.2558
181 H A 0.0000
182 Y A 0.0000
183 A A 0.0000
184 C A 0.0000
185 I A 0.4499
186 R A -0.7308
187 Q A -1.6557
188 K A -2.0161
189 G A -0.8164
190 G A -0.2563
191 Y A 0.5277
192 C A 0.0000
193 S A -0.0876
194 W A 0.4077
195 Y A 1.1356
196 R A -0.9961
197 G A -0.4172
198 W A 1.1101
199 A A 0.1855
200 P A -0.0988
201 P A -0.3432
202 D A -0.8115
203 K A -1.7890
204 S A -0.1212
205 I A 1.4476
206 I A 1.3689
207 N A -1.0098
208 A A -0.2411
209 T A -0.1832
210 D A -0.9329
211 P A -0.4073
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, -0.0365 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_4 -0.0365 View CSV PDB
model_11 -0.0372 View CSV PDB
model_8 -0.0553 View CSV PDB
model_3 -0.0605 View CSV PDB
model_10 -0.0707 View CSV PDB
CABS_average -0.0752 View CSV PDB
model_1 -0.0773 View CSV PDB
model_2 -0.0825 View CSV PDB
model_9 -0.0826 View CSV PDB
model_5 -0.0967 View CSV PDB
model_0 -0.0967 View CSV PDB
model_6 -0.0984 View CSV PDB
input -0.1035 View CSV PDB
model_7 -0.1078 View CSV PDB