Project name: a7ac8971fae8f00

Status: done

Started: 2020-11-20 05:18:49
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                                                (00:07:32)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (01:27:52)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (01:27:55)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (01:27:58)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (01:28:01)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (01:28:04)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (01:28:07)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (01:28:09)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (01:28:12)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (01:28:15)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (01:28:18)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (01:28:21)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (01:28:24)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (01:28:27)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (01:28:30)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (01:28:31)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (01:28:31)
[INFO]       Main:     Simulation completed successfully.                                          (01:28:34)
Show buried residues

Minimal score value
-3.7649
Maximal score value
2.0152
Average score
-0.8291
Total score value
-253.7144

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 -1.3255
17 R X -1.3140
18 G X -0.8581
19 S X -0.5391
20 A X -0.8201
21 S X -0.6956
22 M X 0.0000
23 S X -1.0954
24 D X -1.7903
25 S X -1.5136
26 E X -1.8729
27 V X 0.0000
28 N X -1.9487
29 Q X 0.0000
30 E X -1.4922
31 A X 0.0000
32 K X -2.1455
33 P X -1.2567
34 E X -0.9658
35 V X 0.0672
36 K X -0.4449
37 P X -0.5638
38 E X 0.0000
39 V X 0.1713
40 K X -0.8275
41 P X -1.3359
42 E X -2.2506
43 T X -1.7024
44 H X -2.1736
45 I X 0.0000
46 N X -1.0781
47 L X 0.0000
48 K X -0.8991
49 V X 0.0000
50 S X -1.3825
51 D X -2.1358
52 G X -1.5522
53 S X -1.1503
54 S X -1.4921
55 E X -1.8051
56 I X 0.0983
57 F X 1.1771
58 F X 0.2462
59 K X -1.4775
60 I X -1.2417
61 K X -2.4161
62 K X 0.0000
63 T X -0.8726
64 T X 0.0000
65 P X 0.0000
66 L X 0.0000
67 R X -2.9604
68 R X -3.2751
69 L X 0.0000
70 M X 0.0000
71 E X -3.6731
72 A X -2.5389
73 F X -2.1978
74 A X 0.0000
75 K X -3.7649
76 R X -3.0126
77 Q X -2.8004
78 G X -2.9977
79 K X -3.6901
80 E X -3.5831
81 M X -2.8363
82 D X -2.7362
83 S X -1.8510
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 -0.6042
90 G X 0.0000
91 I X 0.0000
92 R X -0.6843
93 I X 0.0000
94 Q X -1.4701
95 A X -2.1606
96 D X -2.6290
97 Q X -2.4358
98 T X 0.0000
99 P X -1.2031
100 E X -0.7513
101 D X -0.8968
102 L X 0.0000
103 D X 0.0000
104 M X 0.0000
105 E X 0.0000
106 D X -1.3499
107 N X -0.7784
108 D X 0.0000
109 I X 0.3111
110 I X 0.0000
111 E X -1.0009
112 A X 0.0000
113 H X -1.7560
114 R X -2.6833
115 E X 0.0000
116 Q X -1.4003
117 I X 0.0245
118 G X -0.4565
119 G X -0.5099
120 K X 0.0000
121 M X 0.0000
122 E X -1.2269
123 N X -1.0231
124 P X -1.0709
125 S X 0.0000
126 T X 0.0000
127 V X -1.4967
128 Q X -2.0975
129 R X -2.4683
130 G X -1.0715
131 L X 0.1386
132 N X -1.2839
133 G X -1.4164
134 E X -1.7150
135 P X -1.3437
136 I X 0.0000
137 F X -0.6944
138 D X -1.7809
139 P X 0.0000
140 F X -0.5323
141 K X -2.0397
142 G X -1.4249
143 F X -0.8966
144 G X -0.8733
145 L X 0.0000
146 T X 0.0000
147 G X 0.0000
148 N X -1.6123
149 A X -0.7825
150 P X -0.7527
151 T X -0.8327
152 D X -1.3289
153 W X 0.0000
154 N X -2.2347
155 E X -2.1494
156 I X 0.0000
157 K X -1.3438
158 G X -0.9005
159 K X -0.6393
160 V X 0.9653
161 P X 0.2474
162 V X 0.6635
163 E X -0.3413
164 V X 1.6179
165 V X 1.8761
166 Q X -0.0640
167 S X -0.5613
168 P X -0.7128
169 H X -1.4802
170 S X -0.8353
171 P X -0.7435
172 N X -1.0271
173 L X -0.2677
174 Y X 0.0000
175 Q X 0.0000
176 S X 0.0000
177 P X 0.0000
178 H X -1.4502
179 S X -1.0173
180 P X -0.6995
181 N X 0.0000
182 L X 0.0000
183 Y X 0.0421
184 F X 0.0000
185 V X 0.0000
186 L X 0.6534
187 L X 0.0000
188 V X 0.0000
189 P X -0.6618
190 K X -0.2800
191 V X 0.0000
192 V X 1.1506
193 V X 1.7063
194 E X 0.3688
195 Y X 0.4098
196 H X 0.0000
197 Q X -0.8937
198 L X -0.1811
199 D X -1.8509
200 K X -2.2361
201 V X -1.0497
202 V X -1.0085
203 K X -0.3795
204 E X -0.6928
205 S X 0.0000
206 L X -0.1470
207 E X -1.2503
208 V X -0.2261
209 E X -1.6627
210 A X -0.9650
211 T X -0.9925
212 D X -1.7610
213 S X -0.4192
214 F X 0.6313
215 D X -0.5259
216 P X -0.6453
217 T X -1.1368
218 K X -2.4196
219 R X -2.4215
220 L X -0.8327
221 Q X -2.2259
222 K X -2.3610
223 D X -1.9914
224 S X -1.7212
225 P X -1.2154
226 M X -0.8847
227 K X -1.6139
228 D X 0.0000
229 S X -1.1279
230 T X -0.8804
231 R X 0.0000
232 E X -1.1743
233 S X -1.5891
234 Q X -1.4770
235 E X -1.0303
236 K X -1.3811
237 L X 1.1211
238 S X 1.4250
239 L X 2.0152
240 A X -0.0190
241 D X -1.3473
242 G X -1.5955
243 G X -0.9155
244 S X -0.1767
245 M X 0.5258
246 S X 0.0657
247 S X -0.9848
248 G X -1.6578
249 G X -1.3551
250 A X -0.5961
251 T X -0.3622
252 S X -1.2110
253 T X -1.8806
254 R X -2.8131
255 K X -2.7112
256 A X -0.8729
257 L X 1.3349
258 K X 0.0000
259 I X 1.9287
260 E X 0.0000
261 V X 0.5374
262 E X 0.0000
263 K X -1.7344
264 Q X -1.8165
265 S X -1.3748
266 G X -1.2203
267 S X -1.0545
268 S X -1.2870
269 D X -1.7087
270 S X -0.8545
271 L X 0.5532
272 L X 0.7544
273 K X -0.0252
274 N X -0.2461
275 D X 0.6641
276 F X 1.3916
277 A X 0.1778
278 K X -1.4950
279 K X 0.0000
280 P X 0.0000
281 L X -0.2107
282 E X 0.0000
283 H X 0.0000
284 K X -2.8427
285 E X -2.6510
286 N X -2.7235
287 S X -1.7186
288 G X -1.4088
289 T X -1.5546
290 E X -1.1319
291 V X 0.2729
292 K X 0.0000
293 L X 1.0951
294 A X 0.3186
295 A X -0.8948
296 S X -1.0854
297 G X -1.1825
298 E X -1.9675
299 F X -1.0798
300 T X -0.9114
301 K X -0.8340
302 A X -0.3933
303 W X -0.2918
304 K X -1.3042
305 P X -0.7149
306 L X 0.2203
307 L X 0.0000
308 K X -1.9311
309 T X -1.8896
310 D X -2.5752
311 E X -2.5647
312 I X 0.0000
313 E X -3.2665
314 K X -3.0940
315 N X 0.0000
316 R X -2.6239
317 G X -1.4728
318 M X -0.3932
319 G X -0.9259
320 A X -0.6972
321 T X -0.3621
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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, -0.8291 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_6 -0.8291 View CSV PDB
model_4 -0.8421 View CSV PDB
model_7 -0.8491 View CSV PDB
model_1 -0.8663 View CSV PDB
model_3 -0.9096 View CSV PDB
model_5 -0.9157 View CSV PDB
model_10 -0.9488 View CSV PDB
model_9 -0.9661 View CSV PDB
model_2 -0.9887 View CSV PDB
model_8 -0.9981 View CSV PDB
model_0 -1.0176 View CSV PDB
model_11 -1.0312 View CSV PDB
input -1.2148 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018