Project name: Mod_5574681

Status: done

Started: 2020-11-19 23:26:45
Settings
Chain sequence(s) X: PRGSASMSDSEVNQEAKPEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGKMENPSTVQRGLNGEPIFDPFKGFGLTGNAPTDWNEIKGKVPVEVVQSPHSPNLYQSPHSPNLYFVLLVPKVVVEYHQLDKVVKESLEVEATDSFDPTKRLQKDSPMKDSTRESQEKLSLADGGSMSSGGATSTRKALKIEVEKQSGSSDSLLKNDFAKKPLEHKENSGTEVKLAASGEFTKAWKPLLKTDEIEKNRGMGAT
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                                                (00:07:46)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (01:26:10)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (01:26:13)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (01:26:16)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (01:26:19)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (01:26:22)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (01:26:24)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (01:26:27)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (01:26:30)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (01:26:33)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (01:26:36)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (01:26:39)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (01:26:42)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (01:26:45)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (01:26:49)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (01:26:50)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (01:26:50)
[INFO]       Main:     Simulation completed successfully.                                          (01:26:53)
Show buried residues

Minimal score value
-4.2814
Maximal score value
2.5063
Average score
-0.8171
Total score value
-250.0234

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
16 P X -0.5548
17 R X 0.0000
18 G X -0.1341
19 S X -0.0740
20 A X 0.0034
21 S X -0.2211
22 M X 0.6357
23 S X -0.1612
24 D X -0.5022
25 S X -0.9520
26 E X 0.0000
27 V X -0.8111
28 N X -2.1347
29 Q X -2.3285
30 E X -2.5509
31 A X -1.4336
32 K X -1.2350
33 P X -1.1705
34 E X -1.5068
35 V X 0.1436
36 K X -0.8518
37 P X -0.5816
38 E X -0.0750
39 V X 1.1521
40 K X 0.0000
41 P X -0.2675
42 E X 0.0000
43 T X 0.0000
44 H X -2.5931
45 I X 0.0000
46 N X -1.8947
47 L X 0.0000
48 K X -0.6880
49 V X 0.0000
50 S X -1.2338
51 D X -1.9315
52 G X -1.4232
53 S X -1.4567
54 S X -2.0027
55 E X -1.6631
56 I X -0.2209
57 F X 1.1985
58 F X -0.1229
59 K X -2.0971
60 I X 0.0000
61 K X -2.6487
62 K X -2.0814
63 T X -1.7261
64 T X 0.0000
65 P X -1.8217
66 L X 0.0000
67 R X -2.9674
68 R X -2.9632
69 L X 0.0000
70 M X 0.0000
71 E X -3.0511
72 A X -2.6679
73 F X 0.0000
74 A X 0.0000
75 K X -4.2049
76 R X -3.9412
77 Q X -3.7211
78 G X -3.2763
79 K X -3.8514
80 E X -3.5650
81 M X -1.7249
82 D X -1.9898
83 S X -0.9046
84 L X 0.0000
85 R X 0.0000
86 F X 0.0000
87 L X 0.0000
88 Y X 0.0000
89 D X 0.0000
90 G X 0.0000
91 I X -0.3853
92 R X -0.3577
93 I X 0.0000
94 Q X -1.3994
95 A X -1.8153
96 D X -2.6961
97 Q X -1.7692
98 T X -1.2844
99 P X -1.4632
100 E X -1.9253
101 D X 0.0000
102 L X -1.2608
103 D X -1.7327
104 M X -1.2802
105 E X -2.8598
106 D X -2.5080
107 N X -2.5027
108 D X -1.2954
109 I X -0.3448
110 I X 0.0000
111 E X -1.4977
112 A X 0.0000
113 H X -1.5649
114 R X -1.9956
115 E X 0.0000
116 Q X -0.6416
117 I X 0.4455
118 G X -0.0898
119 G X 0.0000
120 K X 0.0000
121 M X 0.0000
122 E X -1.0533
123 N X -1.6323
124 P X -0.9579
125 S X 0.0000
126 T X 0.0000
127 V X -0.7735
128 Q X -1.9657
129 R X -2.5002
130 G X -1.5271
131 L X -0.3681
132 N X -1.3612
133 G X -1.2762
134 E X -1.2217
135 P X 0.0000
136 I X -0.6300
137 F X 0.0000
138 D X -1.9328
139 P X -1.2694
140 F X -0.6330
141 K X -1.5160
142 G X -0.4703
143 F X 1.1868
144 G X 0.3187
145 L X 0.3003
146 T X -0.4935
147 G X -1.1007
148 N X -1.3442
149 A X -0.8937
150 P X -0.7014
151 T X -0.9364
152 D X -1.3891
153 W X -0.4869
154 N X -1.5198
155 E X -1.5919
156 I X 0.0000
157 K X -1.3466
158 G X -0.9989
159 K X -0.4233
160 V X 0.8194
161 P X 1.0892
162 V X 1.3789
163 E X 0.4874
164 V X 2.1764
165 V X 1.9864
166 Q X 0.0000
167 S X 0.0000
168 P X -0.6979
169 H X 0.0000
170 S X 0.0000
171 P X -0.1840
172 N X 0.0000
173 L X 2.1979
174 Y X 0.0000
175 Q X 0.0000
176 S X 0.0000
177 P X 0.0000
178 H X -0.5165
179 S X -0.1981
180 P X -0.5750
181 N X -0.3962
182 L X 0.0000
183 Y X 0.9245
184 F X 2.2294
185 V X 0.0000
186 L X 1.7041
187 L X 0.0000
188 V X 0.6214
189 P X 0.0000
190 K X -1.4345
191 V X -0.6508
192 V X 0.0000
193 V X 0.0705
194 E X -0.7653
195 Y X 0.0000
196 H X -0.7709
197 Q X -1.1427
198 L X 0.0825
199 D X 0.0000
200 K X -1.0019
201 V X 1.1584
202 V X 0.9699
203 K X -0.8798
204 E X -0.8403
205 S X -0.6225
206 L X -0.1322
207 E X -0.8692
208 V X -0.4447
209 E X -1.6243
210 A X -0.9500
211 T X -1.1722
212 D X -1.8878
213 S X -1.0993
214 F X -0.8177
215 D X 0.0000
216 P X 0.0000
217 T X 0.0000
218 K X -1.4381
219 R X -1.8265
220 L X -1.0013
221 Q X -2.1586
222 K X -2.7172
223 D X -1.9629
224 S X -1.6000
225 P X -1.3399
226 M X -1.7862
227 K X -2.4238
228 D X -2.3091
229 S X -1.8831
230 T X 0.0000
231 R X -1.0456
232 E X -0.6478
233 S X -0.7183
234 Q X -0.1627
235 E X 0.0000
236 K X 0.0000
237 L X 0.0000
238 S X 0.0000
239 L X 1.3588
240 A X -0.1988
241 D X -1.3305
242 G X -1.0337
243 G X -0.9837
244 S X -0.3743
245 M X 0.3812
246 S X -0.2736
247 S X -1.1525
248 G X -1.6062
249 G X -1.3385
250 A X -0.7333
251 T X -1.2794
252 S X -1.2216
253 T X -1.4173
254 R X -1.7846
255 K X -1.5468
256 A X 0.3904
257 L X 1.9129
258 K X 1.5304
259 I X 2.5063
260 E X 0.8972
261 V X 0.9408
262 E X -1.1973
263 K X -2.0855
264 Q X -1.5456
265 S X -1.4904
266 G X -1.3941
267 S X -0.8834
268 S X -1.0850
269 D X -1.6363
270 S X 0.0000
271 L X 0.0000
272 L X -0.2778
273 K X -0.4684
274 N X 0.2232
275 D X 0.0000
276 F X 1.4821
277 A X -0.4409
278 K X -2.1549
279 K X -1.5507
280 P X -1.1822
281 L X -0.7840
282 E X 0.0000
283 H X -2.2646
284 K X -3.0233
285 E X -3.0382
286 N X -2.3776
287 S X -1.5291
288 G X -1.2807
289 T X -1.2485
290 E X -1.6210
291 V X -1.1788
292 K X -1.7934
293 L X -0.0194
294 A X -0.4809
295 A X -0.7366
296 S X -0.9006
297 G X -0.7873
298 E X -0.6590
299 F X 0.7187
300 T X 0.0000
301 K X -1.0944
302 A X -0.2489
303 W X 0.0000
304 K X -0.8756
305 P X -0.3485
306 L X -0.5170
307 L X 0.0000
308 K X -3.0641
309 T X -2.6310
310 D X -3.6669
311 E X -3.8531
312 I X -3.1595
313 E X -4.2814
314 K X -4.2469
315 N X -3.4778
316 R X -3.3341
317 G X 0.0000
318 M X 0.0000
319 G X 0.1059
320 A X 0.2376
321 T X -0.1396
Download PDB file
View in 3Dmol
Play the video

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, -0.8171 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_2 -0.8171 View CSV PDB
model_1 -0.9766 View CSV PDB
model_3 -1.0219 View CSV PDB
model_7 -1.0537 View CSV PDB
model_6 -1.0883 View CSV PDB
model_10 -1.0951 View CSV PDB
model_9 -1.103 View CSV PDB
model_0 -1.1263 View CSV PDB
model_5 -1.1311 View CSV PDB
model_11 -1.1313 View CSV PDB
model_4 -1.1737 View CSV PDB
model_8 -1.1948 View CSV PDB
input -1.2148 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018