Project name: Lab 5

Status: done

Started: 2020-11-20 06:08:02
Settings
Chain sequence(s) X: IGGASTPLPTFSNINVGVKSMITQHLNKENTRWVFTPNSSPDITGAGYRVQSANQKNGIPFDNVKPSNSSTPFNPNSDDNKVTPSGGSSKTTTYTHLPNSISPTSDWINALTFTNRNNPQRNQLLLRSLLGTIPVLINKSGT
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                                                (00:02:06)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:35:58)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:35:59)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:36:00)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:36:01)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:36:02)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:36:03)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:36:03)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:36:04)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:36:05)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:36:06)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:36:07)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:36:08)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:36:09)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:36:10)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:36:10)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:36:11)
[INFO]       Main:     Simulation completed successfully.                                          (00:36:12)
Show buried residues
Minimal score value
-2.9345
Maximal score value
2.6576
Average score
-0.2973
Total score value
-42.2218
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
117 I X 1.6490
118 G X 0.2772
119 G X -0.1417
120 A X 0.0170
121 S X -0.4108
122 T X 0.0000
123 P X -0.0157
124 L X 0.7950
125 P X 0.1934
126 T X 0.0000
127 F X 1.6113
128 S X 0.7326
129 N X 0.6642
130 I X 1.4643
131 N X 1.0010
132 V X 1.6394
133 G X 0.5352
134 V X -0.1434
135 K X -1.7651
136 S X 0.0000
137 M X -1.1066
138 I X 0.0000
139 T X -0.9004
140 Q X -0.8047
141 H X 0.0000
142 L X 0.0000
143 N X -1.7139
144 K X -2.6948
145 E X -2.8888
146 N X -2.2080
147 T X -1.6681
148 R X -1.4562
149 W X -0.4442
150 V X 0.9694
151 F X 0.1660
152 T X -0.5899
153 P X -0.9831
154 N X -1.5447
155 S X -1.1571
156 S X -1.0482
157 P X -1.1465
158 D X -1.4008
159 I X -0.3736
160 T X 0.0000
161 G X 0.0000
162 A X 0.0000
163 G X -0.2719
164 Y X -0.0549
165 R X -0.3890
166 V X -0.3340
167 Q X -1.2111
168 S X -1.5300
169 A X -1.2453
170 N X -1.9470
171 Q X -2.0533
172 K X -2.2631
173 N X 0.0000
174 G X 0.0000
175 I X 0.0000
176 P X -0.0444
177 F X 0.7251
178 D X -0.7654
179 N X 0.0000
180 V X -0.3391
181 K X 0.0000
182 P X -0.8795
183 S X -0.6211
184 N X 0.0000
185 S X 0.3204
186 S X 0.0000
187 T X 0.6006
188 P X 0.6879
189 F X 1.7559
190 N X 0.2985
191 P X -0.6936
192 N X -1.8962
193 S X -1.8523
194 D X -2.3181
195 D X -2.9345
196 N X -2.1827
197 K X -2.3960
198 V X -1.0638
199 T X -0.7928
200 P X -0.6067
201 S X -0.6838
202 G X -0.9482
203 G X -1.0113
204 S X -0.8287
205 S X -1.0379
206 K X -1.3514
207 T X 0.0000
208 T X 0.0000
209 T X 0.0000
210 Y X 0.0000
211 T X -0.9876
212 H X -0.6346
213 L X 0.0000
214 P X 0.0000
215 N X 0.0000
216 S X 0.0000
217 I X 0.0000
218 S X 0.6385
219 P X 0.6732
220 T X 0.0000
221 S X 0.0000
222 D X -0.5387
223 W X 0.0000
224 I X 0.0000
225 N X -0.1763
226 A X 0.0000
227 L X 0.8104
228 T X 0.0000
229 F X 0.0000
230 T X -0.7129
231 N X 0.0000
232 R X 0.0000
233 N X 0.0000
234 N X -1.9712
235 P X -1.6603
236 Q X -1.0934
237 R X -0.8315
238 N X -1.5387
239 Q X -1.3203
240 L X 0.0000
241 L X 1.1736
242 L X 1.9708
243 R X 0.7158
244 S X 1.1753
245 L X 2.6576
246 L X 2.3927
247 G X 0.9694
248 T X 0.2909
249 I X 0.7372
250 P X 0.3227
251 V X 1.1398
252 L X 2.3454
253 I X 1.6960
254 N X 0.0000
255 K X -1.7979
256 S X 0.0000
257 G X -0.9248
258 T X -0.6929
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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, -0.2973 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 -0.2973 View CSV PDB
model_11 -0.2984 View CSV PDB
model_2 -0.3575 View CSV PDB
model_5 -0.3702 View CSV PDB
model_3 -0.4207 View CSV PDB
model_4 -0.4574 View CSV PDB
model_10 -0.476 View CSV PDB
model_7 -0.4761 View CSV PDB
model_8 -0.4968 View CSV PDB
model_0 -0.4991 View CSV PDB
model_9 -0.5633 View CSV PDB
model_1 -0.5909 View CSV PDB
input -0.6279 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018