Project name: step9c

Status: done

Started: 2020-11-20 03:05:07
Settings
Chain sequence(s) X: EQIGGLPWIGNNKPYSNSHTAILSVSSNTPLPTFSNIGVGVKSDITKHLNKENTRWVFTPGSTPDIWTGAGYRKASNNNNGIPFDQVKPSSSSTQFNPSSMENQVTPSGGSSKKTTTYSFLPNNISPTSDWINALTFTNKNNPQRNQLLLRALLGTIPVLINKSGDINDQFNKDSEQKWDKTETKEGNLPGF
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                                                (00:03:53)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:54:57)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:54:59)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:55:00)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:55:01)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:55:03)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:55:04)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:55:05)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:55:06)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:55:08)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:55:09)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:55:11)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:55:12)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:55:13)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:55:15)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:55:16)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:55:16)
[INFO]       Main:     Simulation completed successfully.                                          (00:55:18)
Show buried residues
Minimal score value
-3.1993
Maximal score value
3.1725
Average score
-0.6588
Total score value
-126.4832
Download the table (csv)

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
115 E X -1.2079
116 Q X -1.1261
117 I X 0.0000
118 G X 0.0000
119 G X -0.8847
120 L X 0.0000
121 P X -0.6814
122 W X 0.6898
123 I X 0.0000
124 G X -0.6101
125 N X -1.8961
126 N X -2.2826
127 K X -1.9677
128 P X -1.1074
129 Y X 0.0000
130 S X -1.1649
131 N X -0.9645
132 S X -0.7998
133 H X 0.0000
134 T X 0.3319
135 A X 1.1349
136 I X 2.3123
137 L X 2.3542
138 S X 1.5644
139 V X 1.7911
140 S X 0.3338
141 S X -0.6546
142 N X 0.0000
143 T X 0.0000
144 P X 0.0000
145 L X 0.0000
146 P X 0.0000
147 T X 0.0000
148 F X -0.1474
149 S X 0.0000
150 N X 0.0000
151 I X 0.0492
152 G X 0.0526
153 V X 0.0000
154 G X -1.4124
155 V X 0.0000
156 K X -2.5416
157 S X 0.0000
158 D X -1.7419
159 I X 0.0000
160 T X -0.4358
161 K X -1.5068
162 H X 0.0000
163 L X 0.0000
164 N X -1.8419
165 K X -2.3263
166 E X -3.1993
167 N X -2.6393
168 T X -1.4719
169 R X -1.6444
170 W X 0.0448
171 V X 1.0732
172 F X 0.0000
173 T X 0.3367
174 P X 0.0824
175 G X -0.3763
176 S X -0.6431
177 T X 0.0000
178 P X -1.1309
179 D X -2.3064
180 I X 0.0000
181 W X -1.1574
182 T X 0.0000
183 G X 0.0000
184 A X 0.0000
185 G X 0.0000
186 Y X 0.0000
187 R X 0.0000
188 K X -2.0484
189 A X -1.5344
190 S X -1.3975
191 N X -2.0705
192 N X -2.5670
193 N X -2.5094
194 N X -2.3697
195 G X 0.0000
196 I X 0.0000
197 P X -1.0973
198 F X 0.0000
199 D X -1.9254
200 Q X -1.0154
201 V X 0.0000
202 K X -1.2094
203 P X -0.7647
204 S X -0.8820
205 S X -0.6435
206 S X -0.6558
207 S X -0.5710
208 T X -0.6082
209 Q X -0.9287
210 F X 0.4361
211 N X -0.5440
212 P X 0.0000
213 S X -0.8510
214 S X -0.9493
215 M X -0.8661
216 E X -2.0708
217 N X -1.8294
218 Q X -2.1889
219 V X -1.1852
220 T X -1.5320
221 P X -1.2315
222 S X -0.9054
223 G X -0.9289
224 G X -1.1066
225 S X -1.3563
226 S X -1.6992
227 K X -2.7573
228 K X -2.4797
229 T X -1.3954
230 T X -0.9336
231 T X -0.3560
232 Y X -0.1421
233 S X -0.5223
234 F X 0.0000
235 L X 0.0000
236 P X 0.0000
237 N X -0.6946
238 N X 0.0000
239 I X 0.0000
240 S X 0.0000
241 P X 0.0000
242 T X 0.0000
243 S X -0.6035
244 D X -0.8544
245 W X 0.0750
246 I X 1.0781
247 N X 0.0000
248 A X 0.8970
249 L X 1.0082
250 T X 1.0760
251 F X 0.8665
252 T X 0.0000
253 N X -0.9917
254 K X -1.1587
255 N X 0.0000
256 N X -1.4482
257 P X -1.2524
258 Q X -1.1997
259 R X -1.1360
260 N X -1.3055
261 Q X -1.2055
262 L X 0.0000
263 L X 1.6119
264 L X 2.1925
265 R X 1.4664
266 A X 0.0000
267 L X 3.1725
268 L X 2.7803
269 G X 1.0742
270 T X -0.1103
271 I X 0.0000
272 P X -0.8464
273 V X 0.0000
274 L X 0.0000
275 I X 0.0000
276 N X -2.3721
277 K X -2.9684
278 S X -1.6392
279 G X -1.8203
280 D X -2.4652
281 I X 0.0000
282 N X -2.4587
283 D X -2.5879
284 Q X -1.2934
285 F X 0.0996
286 N X -1.0349
287 K X -2.1332
288 D X -2.2380
289 S X -1.7931
290 E X -2.7146
291 Q X -2.3453
292 K X -2.7911
293 W X 0.0000
294 D X 0.0000
295 K X -1.9198
296 T X 0.0000
297 E X -3.0216
298 T X 0.0000
299 K X -2.5885
300 E X -2.5761
301 G X -2.3990
302 N X -1.4500
303 L X 0.0000
304 P X -0.9211
305 G X -1.6302
306 F X 0.0000
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, -0.6588 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_3 -0.6588 View CSV PDB
model_11 -0.726 View CSV PDB
input -0.7306 View CSV PDB
model_10 -0.7528 View CSV PDB
model_2 -0.7554 View CSV PDB
model_0 -0.7589 View CSV PDB
model_6 -0.7768 View CSV PDB
model_4 -0.785 View CSV PDB
model_1 -0.7893 View CSV PDB
model_5 -0.8145 View CSV PDB
model_9 -0.8459 View CSV PDB
model_8 -0.8568 View CSV PDB
model_7 -0.8614 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018