Project name: Mod_5574681

Status: done

Started: 2020-11-20 00:55:36
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                                                (00:07:40)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (01:24:43)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (01:24:46)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (01:24:48)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (01:24:51)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (01:24:54)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (01:24:57)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (01:25:00)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (01:25:03)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (01:25:06)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (01:25:09)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (01:25:12)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (01:25:16)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (01:25:18)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (01:25:22)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (01:25:23)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (01:25:23)
[INFO]       Main:     Simulation completed successfully.                                          (01:25:27)
Show buried residues

Minimal score value
-4.2979
Maximal score value
1.9875
Average score
-1.0069
Total score value
-308.1064

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 -0.9978
17 R X -2.0273
18 G X -1.3284
19 S X -0.9299
20 A X -0.3865
21 S X -0.2669
22 M X 0.1414
23 S X -1.3089
24 D X -2.3744
25 S X -2.1802
26 E X -2.3886
27 V X -2.0977
28 N X -2.8168
29 Q X -3.4364
30 E X -3.1641
31 A X -2.3315
32 K X -2.8870
33 P X -2.2916
34 E X -1.6584
35 V X -0.9166
36 K X -1.9029
37 P X -1.8329
38 E X -1.8002
39 V X -0.3108
40 K X -1.4213
41 P X -1.3553
42 E X -1.6849
43 T X -1.9392
44 H X -2.2900
45 I X 0.0000
46 N X 0.0000
47 L X 0.0000
48 K X -0.1501
49 V X 0.0000
50 S X -0.9581
51 D X -1.5647
52 G X -1.1775
53 S X -1.1368
54 S X -1.5288
55 E X -1.6064
56 I X -0.0293
57 F X 1.1691
58 F X 0.4809
59 K X -1.0837
60 I X 0.0000
61 K X -2.5360
62 K X -2.2420
63 T X -1.3181
64 T X -1.4572
65 P X -1.9211
66 L X 0.0000
67 R X -3.4302
68 R X -3.1401
69 L X 0.0000
70 M X 0.0000
71 E X -2.7562
72 A X -2.3018
73 F X 0.0000
74 A X 0.0000
75 K X -4.0771
76 R X -3.9277
77 Q X -3.8042
78 G X -3.6450
79 K X -3.6436
80 E X -3.3244
81 M X -1.4373
82 D X 0.0000
83 S X -0.8566
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 0.1306
92 R X -0.5915
93 I X 0.0000
94 Q X -1.1763
95 A X -1.6043
96 D X -2.4054
97 Q X -2.0000
98 T X -1.8418
99 P X 0.0000
100 E X -2.9142
101 D X -2.7835
102 L X -1.8160
103 D X -1.7423
104 M X 0.0000
105 E X 0.0000
106 D X 0.0000
107 N X -0.6891
108 D X 0.0000
109 I X 0.5125
110 I X 0.0000
111 E X -0.5741
112 A X -0.8324
113 H X -1.3635
114 R X -1.9897
115 E X -1.6500
116 Q X -0.9502
117 I X 0.9848
118 G X 0.0910
119 G X -0.8227
120 K X 0.0000
121 M X 0.0000
122 E X -1.7064
123 N X -0.9497
124 P X 0.0000
125 S X -0.8090
126 T X 0.0000
127 V X 0.0000
128 Q X -1.0152
129 R X -1.8473
130 G X -0.9155
131 L X 0.1068
132 N X -0.8108
133 G X -0.1864
134 E X -0.1942
135 P X 0.0000
136 I X 1.1344
137 F X 0.7394
138 D X -0.0830
139 P X -0.3654
140 F X 0.0000
141 K X 0.1731
142 G X 0.5322
143 F X 1.5535
144 G X 0.6880
145 L X 0.0618
146 T X -0.5566
147 G X -0.7268
148 N X -1.0746
149 A X -0.6077
150 P X -0.6828
151 T X -1.4525
152 D X -2.5422
153 W X 0.0000
154 N X -2.8600
155 E X -2.9540
156 I X 0.0000
157 K X -2.7329
158 G X -1.8034
159 K X -1.3144
160 V X -0.4308
161 P X 0.1617
162 V X 1.2132
163 E X 0.1788
164 V X 1.8484
165 V X 1.8857
166 Q X 0.8752
167 S X -0.0536
168 P X -1.0502
169 H X -1.8699
170 S X 0.0000
171 P X -0.6011
172 N X 0.2981
173 L X 1.7607
174 Y X 0.0000
175 Q X 0.0000
176 S X -0.0069
177 P X -0.3875
178 H X -0.4911
179 S X -0.3051
180 P X -0.3143
181 N X 0.0000
182 L X 0.0000
183 Y X 1.1079
184 F X 1.9875
185 V X 0.0000
186 L X 1.3717
187 L X 0.0000
188 V X 0.2807
189 P X 0.0000
190 K X -1.4071
191 V X -0.6097
192 V X -0.1117
193 V X -0.3398
194 E X -1.8602
195 Y X -1.1210
196 H X -2.2584
197 Q X -2.3184
198 L X -1.0001
199 D X 0.0000
200 K X -1.9811
201 V X 0.3006
202 V X -0.3046
203 K X -1.2239
204 E X -1.6714
205 S X -0.7958
206 L X -0.2994
207 E X 0.0000
208 V X -0.6008
209 E X -1.5770
210 A X -1.0741
211 T X -0.7262
212 D X -1.9421
213 S X -0.8802
214 F X 0.1062
215 D X -1.1759
216 P X -0.6933
217 T X -0.5427
218 K X -0.6035
219 R X -1.1932
220 L X -0.5800
221 Q X -0.7513
222 K X -2.1977
223 D X -2.4567
224 S X -1.6455
225 P X -1.4520
226 M X -0.7309
227 K X -2.0190
228 D X -2.5714
229 S X -1.6485
230 T X -1.9123
231 R X -3.2013
232 E X -2.4802
233 S X -1.5466
234 Q X -1.8884
235 E X -2.4081
236 K X -2.5636
237 L X 0.0000
238 S X -0.9416
239 L X -0.4619
240 A X -1.0612
241 D X -2.0926
242 G X -1.3215
243 G X -0.9766
244 S X -0.4737
245 M X 0.1177
246 S X -0.1645
247 S X -0.8755
248 G X -0.9024
249 G X -1.1241
250 A X -0.5499
251 T X -0.7283
252 S X -0.8066
253 T X -1.2265
254 R X -1.6932
255 K X -1.8436
256 A X -0.4051
257 L X 0.1887
258 K X -0.7556
259 I X -0.5268
260 E X -2.1968
261 V X -1.9933
262 E X -2.4645
263 K X -2.5046
264 Q X -1.6436
265 S X -1.1939
266 G X -1.3596
267 S X -1.2322
268 S X -1.2872
269 D X -1.7773
270 S X -0.6504
271 L X 0.3849
272 L X -0.1358
273 K X -2.2948
274 N X -2.2639
275 D X -1.9535
276 F X 0.0000
277 A X -1.5696
278 K X -1.8948
279 K X -1.7237
280 P X -1.1796
281 L X -0.5392
282 E X -1.5718
283 H X -2.5512
284 K X -2.8390
285 E X -2.7172
286 N X -1.9629
287 S X -0.8377
288 G X -0.3601
289 T X -0.3759
290 E X -0.2573
291 V X 1.0629
292 K X 0.3788
293 L X 1.4907
294 A X 0.7396
295 A X 0.1295
296 S X -0.3590
297 G X -1.2397
298 E X -1.5513
299 F X -0.7824
300 T X -0.5752
301 K X -0.9229
302 A X -0.5473
303 W X 0.3343
304 K X -1.3626
305 P X -0.3648
306 L X 0.0788
307 L X -1.4288
308 K X -2.9319
309 T X -2.6082
310 D X -3.3213
311 E X -3.6672
312 I X 0.0000
313 E X -4.2979
314 K X -4.2595
315 N X -3.3083
316 R X -3.4740
317 G X -2.0061
318 M X -1.0349
319 G X -2.1049
320 A X -1.3758
321 T X 0.0923
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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, -1.0069 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 -1.0069 View CSV PDB
model_5 -1.021 View CSV PDB
model_1 -1.0291 View CSV PDB
model_0 -1.0438 View CSV PDB
model_4 -1.0701 View CSV PDB
model_6 -1.104 View CSV PDB
model_10 -1.1495 View CSV PDB
model_3 -1.1688 View CSV PDB
model_9 -1.1705 View CSV PDB
model_2 -1.1756 View CSV PDB
model_7 -1.2021 View CSV PDB
input -1.2148 View CSV PDB
model_11 -1.2293 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018