Project name: Tiffany A Veeder

Status: done

Started: 2020-11-19 23:04:49
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                                                (00:07:41)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (01:28:14)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (01:28:16)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (01:28:19)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (01:28:22)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (01:28:25)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (01:28:28)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (01:28:31)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (01:28:34)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (01:28:37)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (01:28:40)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (01:28:43)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (01:28:46)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (01:28:49)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (01:28:53)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (01:28:54)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (01:28:54)
[INFO]       Main:     Simulation completed successfully.                                          (01:28:57)
Show buried residues
Minimal score value
-3.3705
Maximal score value
1.4854
Average score
-0.8838
Total score value
-270.454
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
16 P X -1.0914
17 R X -1.6819
18 G X -1.1913
19 S X -0.7318
20 A X -0.3091
21 S X -0.4406
22 M X -0.2474
23 S X -0.8406
24 D X -1.2977
25 S X -1.1264
26 E X -1.1637
27 V X -0.2308
28 N X 0.0000
29 Q X 0.0000
30 E X 0.0000
31 A X -0.8716
32 K X -1.7377
33 P X -1.0368
34 E X -0.6984
35 V X 0.4739
36 K X -0.2792
37 P X -0.2571
38 E X -0.0057
39 V X 0.8344
40 K X -0.4884
41 P X -0.6249
42 E X 0.0000
43 T X -0.9078
44 H X -1.6996
45 I X 0.0000
46 N X -1.3915
47 L X 0.0000
48 K X -0.3766
49 V X 0.0000
50 S X -1.2841
51 D X -2.1148
52 G X -1.6929
53 S X -1.1224
54 S X -1.3714
55 E X -1.5669
56 I X 0.7809
57 F X 1.4854
58 F X 0.6462
59 K X -1.6122
60 I X -1.5796
61 K X -2.2378
62 K X 0.0000
63 T X -0.9901
64 T X -1.5377
65 P X -1.6280
66 L X 0.0000
67 R X -3.3679
68 R X -3.1054
69 L X -1.9329
70 M X -2.3471
71 E X -3.1022
72 A X -2.3395
73 F X -1.8907
74 A X -2.8169
75 K X -3.2119
76 R X -3.1499
77 Q X -2.7116
78 G X -2.4426
79 K X -2.2457
80 E X -1.9517
81 M X -0.7115
82 D X -1.5513
83 S X -1.5729
84 L X 0.0000
85 R X 0.0000
86 F X 0.0000
87 L X -0.6690
88 Y X 0.0000
89 D X 0.0000
90 G X 0.0000
91 I X 0.0000
92 R X -1.0205
93 I X 0.0000
94 Q X -1.8830
95 A X -1.2511
96 D X -1.4956
97 Q X -1.9225
98 T X -1.5141
99 P X 0.0000
100 E X -1.7840
101 D X -2.1454
102 L X 0.0000
103 D X 0.0000
104 M X 0.0000
105 E X 0.0000
106 D X -1.3449
107 N X -1.1823
108 D X 0.0000
109 I X -0.4756
110 I X 0.0000
111 E X -1.9095
112 A X -1.3971
113 H X -2.0097
114 R X -2.6987
115 E X -1.8406
116 Q X -1.5236
117 I X -0.5201
118 G X -0.7592
119 G X -1.0779
120 K X -0.8684
121 M X 0.0000
122 E X 0.0000
123 N X -2.1486
124 P X 0.0000
125 S X -1.0026
126 T X 0.0000
127 V X 0.0000
128 Q X -1.4547
129 R X 0.0000
130 G X -0.3813
131 L X 0.5370
132 N X -1.0834
133 G X -1.2471
134 E X -1.8229
135 P X -1.2198
136 I X 0.0000
137 F X -0.6959
138 D X -1.2483
139 P X -1.3763
140 F X 0.0000
141 K X -1.4619
142 G X -1.0269
143 F X 0.0000
144 G X -1.0865
145 L X 0.0000
146 T X -1.3189
147 G X -1.4618
148 N X -1.7490
149 A X 0.0000
150 P X -1.2612
151 T X -1.6253
152 D X 0.0000
153 W X 0.0000
154 N X -2.7203
155 E X -2.9132
156 I X -1.9326
157 K X -2.0463
158 G X 0.0000
159 K X -0.0246
160 V X 0.7591
161 P X 0.7204
162 V X 1.3521
163 E X -0.1992
164 V X 1.2084
165 V X 0.4945
166 Q X 0.0000
167 S X 0.0000
168 P X -0.9196
169 H X -1.1180
170 S X -0.6262
171 P X -0.4804
172 N X 0.0000
173 L X 0.2913
174 Y X 0.0000
175 Q X 0.0000
176 S X 0.0000
177 P X -0.2844
178 H X -1.1656
179 S X -0.9548
180 P X 0.0000
181 N X 0.0000
182 L X 0.0000
183 Y X 0.0874
184 F X 0.0000
185 V X 0.0000
186 L X 0.5844
187 L X 0.0000
188 V X 0.0000
189 P X 0.0000
190 K X -0.3223
191 V X -0.1552
192 V X 0.0000
193 V X 0.4667
194 E X -0.3200
195 Y X 0.1112
196 H X -1.2446
197 Q X -1.3624
198 L X 0.0112
199 D X -1.0821
200 K X -1.5582
201 V X -0.2272
202 V X 0.6013
203 K X 0.0000
204 E X -0.9625
205 S X 0.0000
206 L X -1.1008
207 E X -1.2405
208 V X -0.1685
209 E X -1.7376
210 A X -1.0800
211 T X -0.5085
212 D X -0.7562
213 S X 0.2722
214 F X 1.3567
215 D X -0.1008
216 P X -0.2675
217 T X -1.0715
218 K X -1.8811
219 R X -1.7886
220 L X -1.1597
221 Q X -2.0382
222 K X -2.5122
223 D X -2.7655
224 S X -1.4484
225 P X -0.7664
226 M X -0.8330
227 K X 0.0000
228 D X 0.0000
229 S X 0.0000
230 T X -2.0309
231 R X -2.3070
232 E X -2.8008
233 S X -2.2844
234 Q X -2.6761
235 E X -3.0114
236 K X -2.8322
237 L X 0.0000
238 S X 0.0000
239 L X -0.7682
240 A X -1.3644
241 D X -2.2575
242 G X -1.5513
243 G X -0.9521
244 S X -0.4284
245 M X 0.5891
246 S X 0.0569
247 S X -0.5561
248 G X -0.9678
249 G X -1.2855
250 A X -1.0357
251 T X -0.9860
252 S X 0.0000
253 T X 0.0000
254 R X -1.8110
255 K X -2.4695
256 A X -1.2343
257 L X -0.8199
258 K X -0.9359
259 I X 0.6418
260 E X -1.1866
261 V X -0.0813
262 E X -1.5056
263 K X -2.1102
264 Q X -1.9917
265 S X -1.3050
266 G X -1.1001
267 S X -1.0436
268 S X -1.2795
269 D X -1.6728
270 S X -0.9045
271 L X 0.4527
272 L X 0.2700
273 K X -0.7141
274 N X -1.1788
275 D X -1.2411
276 F X -0.5351
277 A X -0.0423
278 K X -0.6002
279 K X -1.6649
280 P X 0.0000
281 L X 0.0000
282 E X 0.0000
283 H X -1.8685
284 K X 0.0000
285 E X -2.9796
286 N X -2.5743
287 S X -1.8741
288 G X -1.6850
289 T X -1.6699
290 E X -2.1899
291 V X -1.7111
292 K X -1.7528
293 L X -1.4190
294 A X -0.2823
295 A X -0.4340
296 S X -0.5943
297 G X -0.8721
298 E X -1.2820
299 F X 0.1287
300 T X -0.2293
301 K X -1.1535
302 A X -0.6004
303 W X -0.3863
304 K X -0.5717
305 P X -0.2116
306 L X 0.1109
307 L X 0.3597
308 K X -0.8404
309 T X -1.3451
310 D X -2.7633
311 E X -2.1991
312 I X -1.3374
313 E X -3.0767
314 K X -3.3705
315 N X -3.0928
316 R X -2.0325
317 G X 0.0000
318 M X 0.0000
319 G X -0.3310
320 A X -0.0999
321 T X -0.0568
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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, -0.8838 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 -0.8838 View CSV PDB
model_2 -0.89 View CSV PDB
model_3 -0.9273 View CSV PDB
model_1 -0.9375 View CSV PDB
model_6 -0.9399 View CSV PDB
model_0 -0.9866 View CSV PDB
model_10 -0.9881 View CSV PDB
model_7 -1.0059 View CSV PDB
model_5 -1.0326 View CSV PDB
model_8 -1.0493 View CSV PDB
model_9 -1.0827 View CSV PDB
model_11 -1.2025 View CSV PDB
input -1.2148 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018