Project name: Gwen Wood

Status: done

Started: 2020-11-18 05:11:49
Settings
Chain sequence(s) X: DHIDPKKMVENYPPSWKTPKWNHHGIWDYNARNLLLQTTGFFNPRRHPEWFDEGQAKADNTSPGFKVGDTDHKKDGFKKNSSSPIALPFEAYFANIGNMVAIGNSVFIFGGNGHATNPLSIGVFRIKYTDNFSKSSVTGWPYAVLFGGLINPQTNGLKDLPLGTNRWFEYVPRMAVSGVKWVGNQLVLAGTLTMGDTATVPRLKYDQLEKHLNLVAQGQGLLREDLQIFTPYGWANRPDIPVGAWLQDEMGSKFGPHYFLNNPDIQDNVNNDTVEALISSYKNTDKLKHVYPYRYSGLYAWQLFNWSNKLTNTPLSANFVNENSYAPNSLFAAILNEDLLTGLSDKIFYGKENEFAENEADRFNQLLSLNPNPNTNWARYLNVVQRFTTGP
input PDB
Selected Chain(s) X
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]                                                (00:00:01)
[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 X chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:08:44)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (02:14:33)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (02:14:38)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (02:14:42)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (02:14:47)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (02:14:51)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (02:14:55)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (02:15:00)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (02:15:03)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (02:15:08)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (02:15:12)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (02:15:16)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (02:15:21)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (02:15:25)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (02:15:30)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (02:15:31)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (02:15:31)
[INFO]       Main:     Simulation completed successfully.                                          (02:15:35)
Show buried residues

Minimal score value
-3.3286
Maximal score value
2.0672
Average score
-0.3955
Total score value
-154.6405

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
1 D X -2.0913
2 H X -1.5936
3 I X 0.3031
4 D X 0.0000
5 P X 0.0145
6 K X -1.4356
7 K X -1.5560
8 M X 0.0000
9 V X -0.3744
10 E X -0.8701
11 N X 0.0000
12 Y X 0.0000
13 P X 0.0000
14 P X -0.3937
15 S X 0.0000
16 W X 0.0000
17 K X -0.6766
18 T X 0.0000
19 P X 0.0000
20 K X 0.0000
21 W X 0.0000
22 N X 0.0000
23 H X 0.0000
24 H X 0.0000
25 G X 0.0000
26 I X 0.0000
27 W X 0.0000
28 D X 0.0000
29 Y X -0.0830
30 N X -0.4727
31 A X 0.0000
32 R X 0.0000
33 N X -0.2317
34 L X 0.3198
35 L X 0.0000
36 L X 0.9362
37 Q X 0.0000
38 T X -0.2309
39 T X 0.0000
40 G X 0.0000
41 F X 0.0000
42 F X 0.0000
43 N X 0.0000
44 P X 0.0000
45 R X -0.5113
46 R X 0.0000
47 H X 0.0000
48 P X -0.8972
49 E X -1.2955
50 W X 0.0000
51 F X 0.0000
52 D X -2.1608
53 E X -2.1807
54 G X 0.0000
55 Q X -2.3176
56 A X -1.5947
57 K X -2.2415
58 A X -1.2707
59 D X -1.4175
60 N X -0.7886
61 T X -0.4325
62 S X -0.4609
63 P X -1.0223
64 G X -1.0806
65 F X -0.9498
66 K X -1.2182
67 V X 0.8168
68 G X -0.2480
69 D X -1.0601
70 T X -1.1903
71 D X -2.3968
72 H X 0.0000
73 K X -2.9999
74 K X -3.3286
75 D X 0.0000
76 G X 0.0000
77 F X 0.0000
78 K X 0.0000
79 K X -2.3021
80 N X -1.5669
81 S X -1.1390
82 S X 0.0000
83 S X -0.4825
84 P X -0.5566
85 I X 0.0000
86 A X -0.2438
87 L X 0.0000
88 P X 0.1648
89 F X 1.3746
90 E X -0.5524
91 A X 0.0000
92 Y X 0.0000
93 F X 2.0640
94 A X 0.4846
95 N X 0.0000
96 I X 0.9624
97 G X -0.1240
98 N X -0.1962
99 M X 0.9131
100 V X 0.0000
101 A X 0.4419
102 I X -0.3053
103 G X -0.7795
104 N X -1.0554
105 S X 0.0000
106 V X 0.7886
107 F X 0.0000
108 I X 0.0000
109 F X 0.0000
110 G X 0.0000
111 G X -0.7483
112 N X -1.7144
113 G X -0.9941
114 H X -0.8076
115 A X -0.4209
116 T X -0.2758
117 N X 0.0000
118 P X -0.6085
119 L X 0.0000
120 S X 0.0000
121 I X 0.0000
122 G X 0.0000
123 V X 0.0000
124 F X 0.0000
125 R X 0.0000
126 I X 0.4900
127 K X -0.3519
128 Y X -0.2130
129 T X -1.1716
130 D X -2.2325
131 N X -1.4042
132 F X 0.4458
133 S X -0.8226
134 K X -1.5832
135 S X -0.9619
136 S X 0.0000
137 V X -0.4220
138 T X 0.0000
139 G X 0.0000
140 W X 0.0000
141 P X 0.0000
142 Y X 0.0000
143 A X 0.0000
144 V X 0.0000
145 L X 0.0000
146 F X 0.0000
147 G X 0.0000
148 G X 0.0000
149 L X 0.0000
150 I X 0.0825
151 N X -1.1009
152 P X 0.0000
153 Q X -1.8595
154 T X -1.3460
155 N X -1.2256
156 G X -1.2021
157 L X -1.2665
158 K X -2.4460
159 D X -2.5608
160 L X 0.0000
161 P X -0.7474
162 L X 0.0000
163 G X 0.0000
164 T X 0.0000
165 N X 0.0000
166 R X 0.0000
167 W X 0.0000
168 F X 0.0000
169 E X 0.0000
170 Y X 0.0000
171 V X 0.0000
172 P X 0.0000
173 R X 0.0000
174 M X 0.0000
175 A X 0.0000
176 V X 0.0000
177 S X -0.8951
178 G X -0.3639
179 V X -0.1399
180 K X -0.5055
181 W X 0.9274
182 V X 1.2237
183 G X -0.1895
184 N X -1.3985
185 Q X -0.9717
186 L X 0.0000
187 V X 0.0137
188 L X 0.0000
189 A X 0.0083
190 G X 0.0000
191 T X 0.3085
192 L X 0.0000
193 T X 0.0816
194 M X 0.0000
195 G X 0.0000
196 D X -0.3571
197 T X 0.0000
198 A X 0.0000
199 T X 0.0000
200 V X 0.0000
201 P X 0.0000
202 R X 0.0000
203 L X 0.0000
204 K X 0.0000
205 Y X 0.1926
206 D X -1.3994
207 Q X -1.5138
208 L X -1.0909
209 E X -2.3805
210 K X -2.1906
211 H X 0.0000
212 L X 0.1918
213 N X -0.9274
214 L X -0.1276
215 V X 0.0000
216 A X -0.4182
217 Q X -0.7580
218 G X 0.0000
219 Q X -0.3367
220 G X 0.0701
221 L X 1.3622
222 L X 1.0351
223 R X 0.0000
224 E X -0.9477
225 D X 0.0000
226 L X 1.1912
227 Q X 0.0000
228 I X 1.6032
229 F X 0.0000
230 T X 0.5249
231 P X 0.0000
232 Y X 0.0970
233 G X 0.0000
234 W X 0.0000
235 A X 0.0000
236 N X 0.0000
237 R X 0.0000
238 P X 0.0000
239 D X 0.0000
240 I X 0.0000
241 P X -0.2232
242 V X 0.0000
243 G X -0.6819
244 A X -0.5462
245 W X -0.1294
246 L X 0.3573
247 Q X -1.2497
248 D X -1.9722
249 E X 0.0000
250 M X -0.3975
251 G X -0.9637
252 S X -1.1635
253 K X -0.9266
254 F X 1.1423
255 G X 0.5930
256 P X 0.5086
257 H X 0.3607
258 Y X 0.0000
259 F X 0.5335
260 L X 0.7230
261 N X -0.0121
262 N X 0.0000
263 P X -0.2888
264 D X -1.1112
265 I X 0.5314
266 Q X -1.0515
267 D X -2.1496
268 N X -1.5948
269 V X 0.0000
270 N X -3.1181
271 N X -3.0257
272 D X -3.3120
273 T X -2.0181
274 V X 0.0000
275 E X -2.5220
276 A X -0.8488
277 L X 0.2701
278 I X 1.0002
279 S X 0.0000
280 S X -0.7909
281 Y X -0.9303
282 K X -1.8846
283 N X -1.1108
284 T X -0.3605
285 D X 0.0000
286 K X -0.4558
287 L X 0.0000
288 K X -0.4978
289 H X 0.0000
290 V X 0.0000
291 Y X 1.5339
292 P X 1.3240
293 Y X 1.1762
294 R X -0.6303
295 Y X 0.0000
296 S X 0.0000
297 G X 0.0000
298 L X 0.5042
299 Y X 1.5599
300 A X 1.2086
301 W X 0.6309
302 Q X 0.0000
303 L X 1.4881
304 F X 2.0672
305 N X 0.0000
306 W X 0.0000
307 S X 0.0000
308 N X 0.0000
309 K X -0.1117
310 L X 0.0000
311 T X -0.2103
312 N X -0.6592
313 T X -0.5048
314 P X -0.6389
315 L X 0.0000
316 S X 0.0000
317 A X -0.0514
318 N X 0.0000
319 F X 0.0000
320 V X 0.0000
321 N X 0.0000
322 E X 0.0000
323 N X 0.0000
324 S X 0.0000
325 Y X 0.0000
326 A X -0.1807
327 P X -0.3458
328 N X -0.2606
329 S X 0.0000
330 L X 1.2770
331 F X 0.0000
332 A X 0.3351
333 A X 0.0000
334 I X -0.4675
335 L X 0.0000
336 N X -1.9902
337 E X -2.5168
338 D X -2.7209
339 L X 0.0000
340 L X 0.0000
341 T X -1.1914
342 G X -0.8857
343 L X 0.0000
344 S X -0.8194
345 D X -1.6735
346 K X -1.8641
347 I X 0.0000
348 F X 0.8364
349 Y X 0.0000
350 G X -1.0697
351 K X -2.1072
352 E X 0.0000
353 N X -1.4914
354 E X -2.5494
355 F X 0.0000
356 A X -1.6314
357 E X -2.1016
358 N X -2.4690
359 E X -2.7000
360 A X -2.1583
361 D X -1.8827
362 R X 0.0000
363 F X -1.7187
364 N X -1.3459
365 Q X 0.0000
366 L X 0.0000
367 L X 0.0000
368 S X -0.3189
369 L X 0.0916
370 N X -1.2921
371 P X -1.4528
372 N X -2.2921
373 P X -1.7204
374 N X -1.6856
375 T X -0.7888
376 N X -1.1282
377 W X 0.0000
378 A X 0.0000
379 R X -1.5970
380 Y X -0.1056
381 L X -0.8655
382 N X -1.7541
383 V X 0.0000
384 V X 0.0000
385 Q X -1.5033
386 R X -1.4654
387 F X 0.0000
388 T X -0.5420
389 T X -0.4749
390 G X 0.0000
391 P X -1.0785
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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, -0.3955 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_8 -0.3955 View CSV PDB
model_6 -0.4114 View CSV PDB
model_2 -0.4228 View CSV PDB
model_10 -0.4316 View CSV PDB
model_1 -0.4497 View CSV PDB
model_7 -0.4564 View CSV PDB
model_0 -0.4592 View CSV PDB
model_3 -0.4594 View CSV PDB
model_5 -0.4657 View CSV PDB
model_9 -0.4802 View CSV PDB
model_4 -0.4886 View CSV PDB
model_11 -0.4956 View CSV PDB
input -0.557 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018