Project name: VAPB_A_WT_FoldX_Dynamic_D10

Status: done

Started: 2026-08-14 12:32:14
Chain sequence(s) A: MAKVEQVLSLEPQHELKFRGPFTDVVTTNLKLGNPTDRNVCFKVKTTAPRRYCVRPNSGIIDAGASINVSVMLQPFDYDPNEKSKHKFMVQSMFAPTDTSDMEAVWKEAKPEDLMDSKLRCVFELPAENDKPHDVEINKIISTTASKTETPIVSKSLSSSLDDTEVKKVMEECKRLQGEVQRLREENKQFKEEDGLRMRKTVQSNSPISALAPTGKEEGLSTRLLALVVLFFIVGVIIGKIAL
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)                                                   (00:00:02)
[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                                                (00:06:09)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:47:36)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:47:37)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:47:38)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:47:40)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:47:41)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:47:42)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:47:43)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:47:44)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:47:45)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:47:47)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:47:48)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:47:49)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:47:50)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:47:54)
[INFO]       Main:     Simulation completed successfully.                                          (00:47:56)
Show buried residues
Minimal score value
-4.4266
Maximal score value
6.3888
Average score
-0.7991
Total score value
-194.1871
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 0.9277
2 A A -0.3539
3 K A -1.5318
4 V A -0.3883
5 E A -2.0575
6 Q A -1.6228
7 V A -0.3565
8 L A -0.1439
9 S A 0.0701
10 L A 0.1463
11 E A -1.4062
12 P A -1.7096
13 Q A -2.3079
14 H A -2.6951
15 E A -2.8288
16 L A 0.0000
17 K A -3.0330
18 F A 0.0000
19 R A -2.6890
20 G A 0.0000
21 P A 0.0000
22 F A 0.0000
23 T A -0.9609
24 D A -1.1521
25 V A -0.7505
26 V A 0.0000
27 T A -0.7343
28 T A -1.2671
29 N A -1.7754
30 L A 0.0000
31 K A -1.8117
32 L A 0.0000
33 G A -0.6179
34 N A -0.6808
35 P A -1.1560
36 T A -1.6211
37 D A -2.6978
38 R A -2.6170
39 N A -1.9140
40 V A 0.0000
41 C A 0.0000
42 F A 0.0000
43 K A -1.1740
44 V A -0.9246
45 K A -1.8537
46 T A -1.0570
47 T A -0.9493
48 A A -0.9230
49 P A -1.1792
50 R A 0.0000
51 R A -1.3995
52 Y A -0.0462
53 C A 0.2712
54 V A 0.1710
55 R A -0.4006
56 P A -0.4964
57 N A -0.3482
58 S A 0.0000
59 G A 0.0000
60 I A 0.0000
61 I A 0.0000
62 D A -1.6965
63 A A -1.2010
64 G A -0.5886
65 A A -0.5575
66 S A -0.8694
67 I A 0.0000
68 N A -1.6875
69 V A 0.0000
70 S A -0.6276
71 V A 0.0000
72 M A 0.0000
73 L A 0.0000
74 Q A -0.8178
75 P A 0.0000
76 F A 0.4550
77 D A -1.4345
78 Y A -1.8190
79 D A -2.6938
80 P A -2.3620
81 N A -2.7436
82 E A -2.7321
83 K A -3.4558
84 S A -2.4735
85 K A -2.7182
86 H A 0.0000
87 K A -2.2945
88 F A 0.0000
89 M A -1.6549
90 V A 0.0000
91 Q A -1.2317
92 S A 0.0000
93 M A 0.0000
94 F A 0.0000
95 A A 0.0000
96 P A -1.5633
97 T A -0.8337
98 D A -1.6658
99 T A -1.0346
100 S A -0.4573
101 D A 0.0000
102 M A 0.0000
103 E A -0.3309
104 A A -0.4228
105 V A -0.2581
106 W A -1.2825
107 K A -2.4869
108 E A -2.4910
109 A A -1.4876
110 K A 0.0000
111 P A -1.2712
112 E A -2.1064
113 D A 0.0000
114 L A 0.0000
115 M A 0.0000
116 D A -1.2346
117 S A 0.0000
118 K A -2.8964
119 L A 0.0000
120 R A -3.7171
121 C A 0.0000
122 V A -2.6579
123 F A 0.0000
124 E A -2.5739
125 L A -1.5798
126 P A -1.4330
127 A A -1.6645
128 E A -2.8393
129 N A -2.8931
130 D A 0.0000
131 K A -2.4780
132 P A -1.3640
133 H A -1.3714
134 D A -1.4652
135 V A 0.5127
136 E A -0.3661
137 I A 0.3752
138 N A 0.0000
139 K A -1.0732
140 I A -0.0702
141 I A 0.5688
142 S A -0.2603
143 T A -0.4977
144 T A -1.1426
145 A A -0.7046
146 S A -1.2723
147 K A -2.3912
148 T A -2.0149
149 E A -2.2460
150 T A -0.7619
151 P A 0.4944
152 I A 2.3545
153 V A 2.4580
154 S A 0.7122
155 K A 0.1771
156 S A -0.4895
157 L A -0.5856
158 S A -1.5798
159 S A -1.4532
160 S A -1.6760
161 L A 0.0000
162 D A -3.5677
163 D A -3.8198
164 T A -3.0989
165 E A -3.0922
166 V A -2.3832
167 K A -3.9767
168 K A -3.7129
169 V A 0.0000
170 M A -1.7428
171 E A -3.9931
172 E A -3.7092
173 C A -2.7503
174 K A -3.7880
175 R A -4.1179
176 L A -3.0540
177 Q A -3.2231
178 G A -3.0573
179 E A -3.3959
180 V A -2.2284
181 Q A -2.8650
182 R A -3.6696
183 L A -2.2547
184 R A -3.1390
185 E A -4.4266
186 E A -3.9884
187 N A -3.4452
188 K A -4.2537
189 Q A -3.4774
190 F A -1.3987
191 K A -2.3765
192 E A -2.9218
193 E A -2.1305
194 D A -2.0254
195 G A -1.6538
196 L A -1.0058
197 R A -2.2953
198 M A -1.6227
199 R A -2.3529
200 K A -2.3065
201 T A -0.9951
202 V A 0.1414
203 Q A -0.4210
204 S A 0.0554
205 N A -0.3272
206 S A 0.0562
207 P A -0.0992
208 I A 1.4538
209 S A 0.0000
210 A A 0.8512
211 L A 1.2761
212 A A 0.6370
213 P A -0.4006
214 T A -0.6215
215 G A -1.8753
216 K A -3.2528
217 E A -3.4187
218 E A -3.2115
219 G A -1.1978
220 L A 0.2488
221 S A -0.3949
222 T A -0.0837
223 R A 0.0758
224 L A 2.7589
225 L A 3.5642
226 A A 2.7167
227 L A 4.2232
228 V A 5.2373
229 V A 5.5398
230 L A 5.9467
231 F A 5.9138
232 F A 6.3888
233 I A 5.7730
234 V A 5.3685
235 G A 3.6597
236 V A 3.6402
237 I A 3.8505
238 I A 3.3484
239 G A 1.4159
240 K A 0.4883
241 I A 2.3250
242 A A 1.7009
243 L A 1.8209
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, -0.7991 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_9 -0.7991 View CSV PDB
model_2 -0.8637 View CSV PDB
model_6 -0.8902 View CSV PDB
model_4 -0.8925 View CSV PDB
model_8 -0.9007 View CSV PDB
model_10 -0.9066 View CSV PDB
CABS_average -0.9248 View CSV PDB
model_0 -0.9288 View CSV PDB
model_7 -0.9443 View CSV PDB
model_3 -0.9751 View CSV PDB
model_1 -0.991 View CSV PDB
model_5 -0.9939 View CSV PDB
model_11 -1.012 View CSV PDB
input -1.0585 View CSV PDB