Project name: design9c

Status: done

Started: 2020-11-20 02:20:47
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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                                                (00:03:52)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:54:30)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:54:32)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:54:33)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:54:34)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:54:36)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:54:37)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:54:38)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:54:40)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:54:41)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:54:43)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:54:44)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:54:45)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:54:47)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:54:49)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:54:49)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:54:49)
[INFO]       Main:     Simulation completed successfully.                                          (00:54:52)
Show buried residues
Minimal score value
-3.8865
Maximal score value
2.1753
Average score
-0.6587
Total score value
-126.4757
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 -2.6616
116 Q X -1.9759
117 I X 0.0000
118 G X -1.0725
119 G X -1.1348
120 L X 0.0000
121 P X -0.7625
122 W X 0.0000
123 I X -0.7321
124 G X -1.3910
125 N X -1.6206
126 N X -2.1596
127 K X -2.1232
128 P X -1.1130
129 Y X -0.3081
130 S X -0.5324
131 N X 0.0000
132 S X -0.2301
133 H X 0.0000
134 T X 0.0000
135 A X 0.0000
136 I X 1.4810
137 L X 1.7080
138 S X 0.8890
139 V X 0.9959
140 S X -0.2790
141 S X -0.7632
142 N X -1.9394
143 T X -1.3381
144 P X -1.3559
145 L X 0.0000
146 P X 0.0000
147 T X 0.0000
148 F X 0.0000
149 S X -0.8005
150 N X -0.3310
151 I X 0.0708
152 G X -0.0548
153 V X 0.4695
154 G X 0.2127
155 V X 0.0000
156 K X -0.8798
157 S X 0.0000
158 D X -1.4681
159 I X 0.0000
160 T X -1.5806
161 K X -2.0369
162 H X 0.0000
163 L X 0.0000
164 N X -1.3860
165 K X -2.1140
166 E X -3.0983
167 N X -2.3700
168 T X 0.0000
169 R X -1.6917
170 W X 0.5112
171 V X 0.8605
172 F X 0.3534
173 T X -0.2752
174 P X -0.3591
175 G X -0.6784
176 S X -0.6104
177 T X -0.7776
178 P X -0.4367
179 D X -1.0155
180 I X 0.0000
181 W X 0.6639
182 T X 0.0000
183 G X 0.0000
184 A X 0.0000
185 G X 0.0745
186 Y X -0.4352
187 R X -0.8320
188 K X 0.0000
189 A X -0.7982
190 S X -1.0206
191 N X -1.6750
192 N X 0.0000
193 N X -1.3289
194 N X 0.0000
195 G X -1.0210
196 I X 0.0000
197 P X 0.0234
198 F X 0.0000
199 D X -0.9758
200 Q X 0.0000
201 V X 0.0000
202 K X -1.6663
203 P X -1.1766
204 S X -0.9640
205 S X -0.8063
206 S X 0.0000
207 S X -0.2753
208 T X -0.1167
209 Q X -0.2595
210 F X 0.2322
211 N X -0.7726
212 P X -0.6891
213 S X -0.6273
214 S X -0.8970
215 M X -0.1994
216 E X -1.2123
217 N X -1.4684
218 Q X -0.8745
219 V X 0.3352
220 T X -0.5372
221 P X -0.7092
222 S X -0.7568
223 G X -0.8974
224 G X -1.1132
225 S X -0.9283
226 S X -1.4332
227 K X -2.1943
228 K X -2.5721
229 T X -1.5729
230 T X -1.6205
231 T X -1.7482
232 Y X 0.0000
233 S X -0.5429
234 F X 0.6596
235 L X 0.0000
236 P X 0.0000
237 N X 0.0000
238 N X 0.0000
239 I X 0.2196
240 S X -0.3040
241 P X 0.0000
242 T X 0.0000
243 S X 0.0000
244 D X -0.9580
245 W X 0.0000
246 I X -0.1021
247 N X -1.2971
248 A X -0.3152
249 L X -0.4352
250 T X -0.8670
251 F X 0.0000
252 T X 0.0000
253 N X -1.4248
254 K X -2.0331
255 N X -1.7909
256 N X -1.9282
257 P X -1.8056
258 Q X -2.1703
259 R X -2.0945
260 N X -1.9964
261 Q X -1.6257
262 L X -0.6807
263 L X -0.1611
264 L X 1.0905
265 R X 0.1653
266 A X 0.0000
267 L X 2.1414
268 L X 2.1753
269 G X 1.0879
270 T X 0.4652
271 I X 0.0000
272 P X -0.1842
273 V X 0.0000
274 L X 0.0000
275 I X 0.0000
276 N X -1.3261
277 K X -1.8500
278 S X -1.2387
279 G X -1.1314
280 D X -1.4155
281 I X -0.2328
282 N X -1.0119
283 D X -2.1341
284 Q X 0.0000
285 F X 0.0000
286 N X -2.3028
287 K X 0.0000
288 D X -2.5844
289 S X -2.5305
290 E X -3.5252
291 Q X 0.0000
292 K X -2.9330
293 W X 0.0000
294 D X -1.4539
295 K X -2.0108
296 T X 0.0000
297 E X -3.0604
298 T X 0.0000
299 K X -3.8865
300 E X -3.3935
301 G X -2.2496
302 N X -1.7121
303 L X 0.3095
304 P X 0.0000
305 G X 0.6842
306 F X 1.9777
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, -0.6587 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_4 -0.6587 View CSV PDB
model_3 -0.6797 View CSV PDB
model_11 -0.6802 View CSV PDB
model_7 -0.7071 View CSV PDB
model_5 -0.7134 View CSV PDB
model_10 -0.7191 View CSV PDB
input -0.7306 View CSV PDB
model_8 -0.7485 View CSV PDB
model_2 -0.7669 View CSV PDB
model_0 -0.788 View CSV PDB
model_6 -0.8053 View CSV PDB
model_1 -0.8168 View CSV PDB
model_9 -0.844 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018