Project name: 5ba2d299647eca4

Status: done

Started: 2021-10-13 14:35:26
Settings
Chain sequence(s) A: GAKPFGEKKFIEIKGRRMAYIDEGTGDPILFQHGNPTSSYLWRNIMPHCAGLGRLIACDLIGMGDSDKLDPSGPERYAYAEHRDYLDALWEALDLGDRVVLVVHDWGSALGFDWARRHRERVQGIAYMEAIAMPIEWADFPEQDRDLFQAFRSQAGEELVLQDNVFVEQVLPGLILRPLSEAEMAAYREPFLAAGEARRPTLSWPRQIPIAGTPADVVAIARDYAGWLSESPIPKLFINAEPGALTTGRMRDFCRTWPNQTEITVAGAHFIQEDSPDEIGAAIAAFVRRLRPA
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
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 minimalization                                        (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:03:03)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (01:13:36)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (01:13:38)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (01:13:40)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (01:13:43)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (01:13:45)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (01:13:47)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (01:13:49)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (01:13:51)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (01:13:53)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (01:13:55)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (01:13:57)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (01:13:59)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (01:14:01)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (01:14:04)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (01:14:04)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (01:14:05)
[INFO]       Main:     Simulation completed successfully.                                          (01:14:07)
Show buried residues

Minimal score value
-4.2508
Maximal score value
1.1656
Average score
-0.7861
Total score value
-230.3287

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
4 G A -0.8882
5 A A -0.6363
6 K A -1.2068
7 P A -0.8898
8 F A -0.3083
9 G A -1.6217
10 E A -3.0539
11 K A -2.9627
12 K A -2.3549
13 F A -0.4273
14 I A -0.7562
15 E A -1.9132
16 I A -0.8307
17 K A -1.9649
18 G A -1.9388
19 R A 0.0000
20 R A -1.8082
21 M A 0.0000
22 A A -0.5460
23 Y A 0.0000
24 I A 0.0000
25 D A 0.0000
26 E A -1.8529
27 G A -1.4557
28 T A -0.8693
29 G A -1.1969
30 D A 0.0000
31 P A 0.0000
32 I A 0.0000
33 L A 0.0000
34 F A 0.0000
35 Q A 0.0000
36 H A 0.0000
37 G A 0.0000
38 N A 0.0000
39 P A 0.0000
40 T A 0.0000
41 S A 0.0000
42 S A 0.0000
43 Y A 0.3646
44 L A 0.0000
45 W A 0.0000
46 R A -0.6101
47 N A -1.3487
48 I A 0.0000
49 M A 0.0000
50 P A 0.0000
51 H A -1.4191
52 C A 0.0000
53 A A 0.0000
54 G A -0.6690
55 L A -0.6332
56 G A 0.0000
57 R A -1.2083
58 L A 0.0000
59 I A 0.0000
60 A A 0.0000
61 C A 0.0000
62 D A 0.0000
63 L A 0.0000
64 I A 0.0000
65 G A 0.0000
66 M A 0.3311
67 G A -0.6493
68 D A -1.2412
69 S A -1.3480
70 D A -2.3986
71 K A -2.5429
72 L A 0.0000
73 D A -2.0694
74 P A -1.2115
75 S A -1.0027
76 G A -1.1479
77 P A -1.1519
78 E A -1.1800
79 R A 0.0000
80 Y A 0.0000
81 A A -0.7671
82 Y A 0.0000
83 A A -0.8660
84 E A -1.2294
85 H A 0.0000
86 R A -1.1841
87 D A -1.6653
88 Y A 0.0000
89 L A 0.0000
90 D A -1.3676
91 A A -1.2430
92 L A 0.0000
93 W A 0.0000
94 E A -2.1051
95 A A -1.0528
96 L A -0.9157
97 D A -1.7946
98 L A -1.6715
99 G A -1.6625
100 D A -2.2777
101 R A -3.1497
102 V A 0.0000
103 V A 0.0000
104 L A 0.0000
105 V A 0.0000
106 V A 0.0000
107 H A 0.0000
108 D A 0.0000
109 W A 0.0000
110 G A 0.0000
111 S A 0.0000
112 A A 0.0000
113 L A 0.0000
114 G A -0.3936
115 F A 0.0000
116 D A 0.0000
117 W A 0.0000
118 A A 0.0000
119 R A -1.7576
120 R A -2.8828
121 H A -3.0514
122 R A -4.0338
123 E A -4.1924
124 R A -4.2508
125 V A 0.0000
126 Q A -2.0806
127 G A 0.0000
128 I A 0.0000
129 A A 0.0000
130 Y A 0.0000
131 M A 0.0000
132 E A 0.0000
133 A A 0.0000
134 I A 0.0000
135 A A 0.0000
136 M A 0.0000
137 P A -0.8978
138 I A 0.0000
139 E A -1.8450
140 W A -1.2968
141 A A -0.8957
142 D A -1.4622
143 F A 0.0000
144 P A -1.0217
145 E A -0.8526
146 Q A 0.0000
147 D A -1.4521
148 R A -1.9633
149 D A -2.3064
150 L A -1.2130
151 F A 0.0000
152 Q A -1.7054
153 A A -1.5031
154 F A 0.0000
155 R A -1.4818
156 S A -1.1874
157 Q A -1.9909
158 A A -1.2740
159 G A 0.0000
160 E A -1.5233
161 E A -2.1454
162 L A -1.4170
163 V A 0.0000
164 L A -0.3509
165 Q A -1.8788
166 D A -2.5694
167 N A -1.7814
168 V A 0.0000
169 F A 0.0000
170 V A 0.0000
171 E A -1.6180
172 Q A -1.4468
173 V A 0.0000
174 L A 0.0000
175 P A -0.1032
176 G A -0.1741
177 L A 0.0000
178 I A 1.1656
179 L A 0.0000
180 R A -1.2808
181 P A -0.9489
182 L A -0.4070
183 S A -1.0892
184 E A -1.6718
185 A A -0.8700
186 E A 0.0000
187 M A -0.9954
188 A A -1.0980
189 A A 0.0000
190 Y A 0.0000
191 R A -1.5286
192 E A -1.6055
193 P A -0.5014
194 F A 0.0000
195 L A 0.3224
196 A A 0.0151
197 A A -0.1075
198 G A -0.2073
199 E A -1.1577
200 A A 0.0000
201 R A -0.7025
202 R A -0.8459
203 P A 0.0000
204 T A -0.4195
205 L A 0.0000
206 S A 0.0000
207 W A 0.0000
208 P A 0.0000
209 R A -0.9105
210 Q A 0.0000
211 I A 0.0000
212 P A 0.0000
213 I A 0.0000
214 A A -0.6346
215 G A -0.8473
216 T A 0.0000
217 P A -0.8240
218 A A -0.9238
219 D A -1.7225
220 V A 0.0000
221 V A 0.0000
222 A A -1.5070
223 I A -1.3545
224 A A 0.0000
225 R A -2.4939
226 D A -2.4561
227 Y A 0.0000
228 A A 0.0000
229 G A -1.3261
230 W A -0.9505
231 L A 0.0000
232 S A -1.3095
233 E A -1.7059
234 S A -1.2466
235 P A -1.2694
236 I A 0.0000
237 P A -0.7783
238 K A 0.0000
239 L A 0.0000
240 F A 0.0000
241 I A 0.0000
242 N A -1.2479
243 A A 0.0000
244 E A -1.9691
245 P A -0.9030
246 G A -0.8489
247 A A 0.0000
248 L A 0.0000
249 T A 0.0000
250 T A 0.0000
251 G A -1.5338
252 R A -2.1065
253 M A 0.0000
254 R A -2.6007
255 D A -2.9137
256 F A -1.4488
257 C A 0.0000
258 R A -3.0775
259 T A -1.7720
260 W A 0.0000
261 P A -1.4777
262 N A -1.3641
263 Q A -1.5570
264 T A -1.4028
265 E A -2.1584
266 I A -1.0170
267 T A -1.0493
268 V A 0.0000
269 A A -1.2267
270 G A 0.0000
271 A A 0.0000
272 H A 0.0000
273 F A 0.0000
274 I A 0.0000
275 Q A 0.0000
276 E A -1.0773
277 D A 0.0000
278 S A -1.4523
279 P A -1.8174
280 D A -2.9568
281 E A -2.7702
282 I A 0.0000
283 G A 0.0000
284 A A -1.2226
285 A A -1.1124
286 I A 0.0000
287 A A -0.8431
288 A A -1.3005
289 F A 0.0000
290 V A 0.0000
291 R A -3.1828
292 R A -3.2129
293 L A 0.0000
294 R A -2.7819
295 P A -1.8558
296 A A -1.3020
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A3D 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 A3D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A3D score, -0.7861 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 A3D Score
model_0 -0.7861 View CSV PDB
model_11 -0.7957 View CSV PDB
model_2 -0.8049 View CSV PDB
model_7 -0.8097 View CSV PDB
model_1 -0.8222 View CSV PDB
model_3 -0.8337 View CSV PDB
model_6 -0.8532 View CSV PDB
model_10 -0.8555 View CSV PDB
model_8 -0.8754 View CSV PDB
model_4 -0.8756 View CSV PDB
model_9 -0.8761 View CSV PDB
input -0.8801 View CSV PDB
model_5 -0.894 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018