Project name: 1e789e8074d0083

Status: done

Started: 2024-07-18 21:46:31
Chain sequence(s) A: DIQMTQSPSSLSASVGDRVTITCQASQGGSSYLNWYQKKPGKAPKLLIYDASSLETGVPSRFSGSGSGTDFTFTISSLQPEDIATYFCQHGSSLPLAFGGGTKVEIKSGGGGSGGGGSGGGGQVQLQESGPGLVKPSETLSLTCTVSGGSVSSGDYYGSWIRQSPGKGLEWIGHISGSGSTNYSPSLKSRLTISIDTSKTQFSLKLSSVTAADTAIYYCVRDRVTGAGSIWGQGTMVTVSS
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                                          (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:17)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:31:40)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:31:41)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:31:41)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:31:42)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:31:43)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:31:44)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:31:45)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:31:45)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:31:46)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:31:47)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:31:48)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:31:49)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:31:49)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:31:52)
[INFO]       Main:     Simulation completed successfully.                                          (00:31:53)
Show buried residues
Minimal score value
-2.4302
Maximal score value
1.0539
Average score
-0.569
Total score value
-137.1305
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 D A -2.3475
2 I A 0.0000
3 Q A -1.3055
4 M A 0.0000
5 T A -0.8195
6 Q A 0.0000
7 S A -0.6128
8 P A -0.3961
9 S A -0.6211
10 S A -1.0150
11 L A -0.6906
12 S A -1.0425
13 A A -1.1439
14 S A -1.4071
15 V A -1.1259
16 G A -1.4654
17 D A -1.8710
18 R A 0.0000
19 V A 0.0645
20 T A 0.1463
21 I A 0.0000
22 T A -0.5671
23 C A 0.0000
24 Q A -1.6396
25 A A 0.0000
26 S A -1.4796
27 Q A -1.7618
28 G A -1.4596
29 G A -1.4820
30 S A -0.8563
31 S A -0.5989
32 Y A -0.1441
33 L A 0.0000
34 N A 0.0000
35 W A 0.0000
36 Y A 0.0000
37 Q A 0.0000
38 K A -0.3850
39 K A 0.0000
40 P A -0.9443
41 G A -1.1415
42 K A -1.1327
43 A A -0.7729
44 P A 0.0000
45 K A 0.0000
46 L A 0.0000
47 L A 0.0000
48 I A 0.0000
49 Y A 0.0904
50 D A -0.3537
51 A A -0.3300
52 S A -0.3928
53 S A -0.1801
54 L A -0.2740
55 E A -0.4946
56 T A 0.0000
57 G A -0.9140
58 V A -0.6581
59 P A -0.9496
60 S A -1.1438
61 R A -1.9569
62 F A 0.0000
63 S A -0.6603
64 G A -0.5374
65 S A -0.7408
66 G A -1.0361
67 S A -0.9663
68 G A -1.1072
69 T A -1.2376
70 D A -1.6043
71 F A 0.0000
72 T A -0.5897
73 F A 0.0000
74 T A -0.2643
75 I A 0.0000
76 S A -1.2516
77 S A -1.0826
78 L A 0.0000
79 Q A 0.0000
80 P A -1.1824
81 E A -1.5561
82 D A -1.8443
83 I A -0.7006
84 A A 0.0000
85 T A -0.7385
86 Y A 0.0000
87 F A 0.0000
88 C A 0.0000
89 Q A 0.0000
90 H A 0.0000
91 G A 0.0000
92 S A -0.5780
93 S A -0.5748
94 L A 0.0000
95 P A -0.3328
96 L A -0.1414
97 A A 0.0000
98 F A 0.0000
99 G A -1.0194
100 G A 0.0000
101 G A -1.1483
102 T A 0.0000
103 K A -1.2165
104 V A 0.0000
105 E A -2.2081
106 I A -1.7292
107 K A -2.2766
108 S A -1.6016
109 G A -1.2457
110 G A -1.1272
111 G A -0.7781
112 G A -0.7674
113 S A -0.6961
114 G A -0.7553
115 G A -0.9576
116 G A -1.1174
117 G A -0.8908
118 S A 0.0000
119 G A -0.9115
120 G A -1.0844
121 G A -0.9020
122 G A -0.9420
123 Q A -0.5676
124 V A 0.0000
125 Q A -1.5715
126 L A 0.0000
127 Q A -1.8183
128 E A 0.0000
129 S A -0.6589
130 G A 0.0000
131 P A 0.3262
132 G A 0.0000
133 L A 0.9349
134 V A 0.0000
135 K A -2.2503
136 P A -2.0799
137 S A -1.7678
138 E A -2.4302
139 T A -1.5945
140 L A 0.0000
141 S A -0.2811
142 L A 0.0000
143 T A -0.5482
144 C A 0.0000
145 T A -1.1682
146 V A 0.0000
147 S A -1.0695
148 G A -0.5285
149 G A -0.5704
150 S A -0.0232
151 V A 1.0281
152 S A 0.1464
153 S A -0.3659
154 G A -0.8931
155 D A -1.5356
156 Y A -0.9720
157 Y A 0.0000
158 G A 0.0000
159 S A 0.0000
160 W A 0.0000
161 I A 0.0000
162 R A 0.0000
163 Q A -0.4515
164 S A 0.0000
165 P A -1.0970
166 G A -1.4400
167 K A -1.9288
168 G A 0.0000
169 L A 0.0000
170 E A 0.0000
171 W A 0.0000
172 I A 0.0000
173 G A 0.0000
174 H A 0.0000
175 I A 0.0000
176 S A -0.4568
177 G A -0.5742
178 S A -0.8433
179 G A -0.9669
180 S A -0.6717
181 T A -0.3374
182 N A -0.6641
183 Y A 0.0846
184 S A -0.1538
185 P A -0.4891
186 S A -0.3468
187 L A -0.9539
188 K A -1.9788
189 S A 0.0000
190 R A -2.2595
191 L A 0.0000
192 T A -0.5584
193 I A 0.0000
194 S A 0.0233
195 I A 0.2708
196 D A -1.4144
197 T A -1.2448
198 S A -1.3869
199 K A -2.1618
200 T A -1.3208
201 Q A -1.1788
202 F A 0.0000
203 S A -0.2946
204 L A 0.0000
205 K A -1.2519
206 L A 0.0000
207 S A -1.8033
208 S A -1.7239
209 V A 0.0000
210 T A -1.5752
211 A A 0.0000
212 A A 0.0000
213 D A -0.8911
214 T A -0.4499
215 A A 0.0000
216 I A 0.3053
217 Y A 0.0000
218 Y A 0.0000
219 C A 0.0000
220 V A 0.0000
221 R A 0.0000
222 D A 0.0000
223 R A -1.5185
224 V A -0.7414
225 T A -0.5380
226 G A 0.0000
227 A A 0.0000
228 G A 0.0000
229 S A 0.0000
230 I A 0.0000
231 W A 0.0000
232 G A 0.0000
233 Q A -0.8710
234 G A -0.7199
235 T A 0.1242
236 M A 1.0539
237 V A 0.0000
238 T A 0.2031
239 V A 0.0000
240 S A -1.1138
241 S A -0.8866
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, -0.569 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_5 -0.569 View CSV PDB
model_10 -0.5885 View CSV PDB
model_11 -0.5982 View CSV PDB
model_3 -0.5998 View CSV PDB
model_2 -0.6027 View CSV PDB
model_0 -0.6138 View CSV PDB
model_8 -0.6208 View CSV PDB
CABS_average -0.6338 View CSV PDB
model_1 -0.6384 View CSV PDB
input -0.6495 View CSV PDB
model_6 -0.6602 View CSV PDB
model_4 -0.6647 View CSV PDB
model_7 -0.6789 View CSV PDB
model_9 -0.7705 View CSV PDB