Project name: Seli3

Status: done

Started: 2025-07-21 14:42:53
Chain sequence(s) A: QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPDSGGTNYAQKFQGRVTMTRDTSISTAYMELNRLRSDDTAVYYCARDQPLGACTNGVCSYFDYWGQGTLVTVSSGGGGSGGGGSGGGGSGGGGSDIQMTQSPSSVSASVGDRVTITCRASQGIYSWLAWYQQKPGKAPNLLIYTASTLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQANIFPLTFGGGTKVEIK
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage No
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]       runJob:   FoldX not utilized. Treating input pdb file as it was already optimized.    (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:27:31)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:27:32)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:27:33)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:27:34)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:27:35)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:27:36)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:27:36)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:27:37)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:27:38)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:27:39)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:27:40)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:27:40)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:27:41)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:27:45)
[INFO]       Main:     Simulation completed successfully.                                          (00:27:46)
Show buried residues

Minimal score value
-2.4957
Maximal score value
3.1409
Average score
-0.4509
Total score value
-114.0807

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 Q A -0.1049
2 V A 1.0462
3 Q A -0.0176
4 L A 0.0000
5 V A -0.4343
6 Q A 0.0000
7 S A -0.6766
8 G A -0.3134
9 A A 0.3487
10 E A 0.1678
11 V A 0.7362
12 K A -1.3262
13 K A -2.2700
14 P A -2.0646
15 G A -1.7697
16 A A 0.0000
17 S A -1.5864
18 V A 0.0000
19 K A -2.1289
20 V A 0.0000
21 S A -0.9518
22 C A 0.0000
23 K A -1.5482
24 A A 0.0000
25 S A -0.0962
26 G A 0.4176
27 Y A 0.9590
28 T A 0.0000
29 F A 0.0000
30 T A -0.0285
31 G A 0.0000
32 Y A 0.0000
33 Y A 0.0000
34 M A 0.0000
35 H A 0.0000
36 W A 0.0000
37 V A 0.0000
38 R A 0.0000
39 Q A -0.2682
40 A A -0.7661
41 P A -0.9854
42 G A -1.0881
43 Q A -0.7969
44 G A -0.6144
45 L A 0.0000
46 E A 0.0000
47 W A 0.0000
48 M A 0.0000
49 G A 0.0000
50 W A 0.0000
51 I A 0.0000
52 N A 0.0000
53 P A 0.0000
54 D A -1.9796
55 S A -1.3199
56 G A -1.2885
57 G A -0.8840
58 T A -0.5103
59 N A -0.1999
60 Y A 0.1968
61 A A -0.1903
62 Q A -1.3157
63 K A -1.2558
64 F A 0.0000
65 Q A -1.6263
66 G A -1.4477
67 R A -1.8338
68 V A 0.0000
69 T A -1.1509
70 M A -0.5965
71 T A -0.5694
72 R A -1.3146
73 D A -1.4929
74 T A -1.0030
75 S A -0.3698
76 I A 0.1526
77 S A -0.5605
78 T A 0.0000
79 A A 0.0000
80 Y A -0.6332
81 M A 0.0000
82 E A -1.6736
83 L A 0.0000
84 N A -2.1147
85 R A 0.0000
86 L A 0.0000
87 R A -2.2087
88 S A -1.9573
89 D A -2.4957
90 D A -1.7297
91 T A -0.5232
92 A A 0.0000
93 V A 0.0000
94 Y A 0.0000
95 Y A 0.0000
96 C A 0.0000
97 A A 0.0000
98 R A 0.0000
99 D A 0.0000
100 Q A 0.2509
101 P A 0.5997
102 L A 1.1224
103 G A 0.0599
104 A A -0.0706
105 C A -0.3692
106 T A -0.6146
107 N A -1.3599
108 G A 0.0451
109 V A 1.1552
110 C A 0.7529
111 S A 0.3511
112 Y A 0.0000
113 F A 0.0000
114 D A -0.0303
115 Y A 0.7223
116 W A 0.3847
117 G A -0.2834
118 Q A -0.5696
119 G A -0.2109
120 T A 0.0000
121 L A 1.5748
122 V A 0.0000
123 T A -0.1197
124 V A 0.0000
125 S A -1.4770
126 S A -1.7319
127 G A -1.5629
128 G A -1.5164
129 G A -1.5594
130 G A -1.2803
131 S A -1.3478
132 G A -1.5159
133 G A -1.4832
134 G A -1.3487
135 G A -1.2250
136 S A -1.5617
137 G A -1.7054
138 G A -1.5656
139 G A -1.3630
140 G A 0.0000
141 S A -0.8558
142 G A -0.5834
143 G A -0.7104
144 G A -0.7803
145 G A 0.0000
146 S A -1.4181
147 D A -1.2076
148 I A 0.0000
149 Q A -1.2022
150 M A 0.0000
151 T A -1.0973
152 Q A -1.0104
153 S A -0.8500
154 P A -0.5263
155 S A -0.6122
156 S A -0.8464
157 V A -0.7377
158 S A -0.9438
159 A A 0.0000
160 S A -0.7226
161 V A 0.4934
162 G A -0.5994
163 D A -1.5378
164 R A -0.8511
165 V A 0.0000
166 T A -0.3694
167 I A 0.0000
168 T A -0.7311
169 C A 0.0000
170 R A -2.2685
171 A A 0.0000
172 S A -1.4023
173 Q A -1.6919
174 G A -0.2680
175 I A 1.1268
176 Y A 0.8588
177 S A 0.5112
178 W A 1.7391
179 L A 0.0000
180 A A 0.0000
181 W A 0.0000
182 Y A 0.0000
183 Q A 0.0000
184 Q A 0.0000
185 K A -1.2162
186 P A -1.0795
187 G A -1.1324
188 K A -1.0717
189 A A 0.0000
190 P A 0.0000
191 N A 0.0000
192 L A -0.0005
193 L A 0.0000
194 I A 0.0000
195 Y A 0.0000
196 T A -0.0277
197 A A 0.0146
198 S A -0.2318
199 T A -0.1333
200 L A -0.3637
201 Q A -0.7788
202 S A -0.9852
203 G A -0.7740
204 V A 0.0000
205 P A -0.9094
206 S A 0.0000
207 R A -2.0675
208 F A 0.0000
209 S A -0.7118
210 G A -0.5845
211 S A -0.6372
212 G A -1.0482
213 S A -0.9858
214 G A -0.7374
215 T A -0.8812
216 D A -1.4266
217 F A -1.0183
218 T A -0.6847
219 L A 0.0000
220 T A -0.4341
221 I A 0.0000
222 S A -0.6845
223 S A -0.5174
224 L A -0.3289
225 Q A -0.8477
226 P A -1.3805
227 E A -2.2034
228 D A -1.5210
229 F A 0.1091
230 A A 0.0000
231 T A -0.6552
232 Y A 0.0000
233 Y A 0.0000
234 C A 0.0000
235 Q A 0.0000
236 Q A 0.0000
237 A A 0.0000
238 N A 1.6861
239 I A 3.1409
240 F A 2.8073
241 P A 1.2683
242 L A 0.0000
243 T A 0.0000
244 F A -0.0952
245 G A 0.0000
246 G A -0.5619
247 G A -1.0980
248 T A 0.0000
249 K A -1.3753
250 V A 0.0000
251 E A -1.0746
252 I A -1.1699
253 K A -1.6669
Download PDB file
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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, -0.4509 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_6 -0.4509 View CSV PDB
model_2 -0.4701 View CSV PDB
model_5 -0.4792 View CSV PDB
model_7 -0.4887 View CSV PDB
model_11 -0.4902 View CSV PDB
CABS_average -0.5236 View CSV PDB
model_1 -0.5239 View CSV PDB
model_9 -0.5319 View CSV PDB
model_8 -0.5451 View CSV PDB
model_0 -0.5468 View CSV PDB
model_10 -0.5485 View CSV PDB
model_3 -0.5808 View CSV PDB
input -0.5848 View CSV PDB
model_4 -0.6269 View CSV PDB