Project name: Nucleocapsid CTerminal 1 subunit

Status: done

Started: 2020-06-22 22:51:34
Settings
Chain sequence(s) A: KPRQKRTATKAYNVTQAFGRRGPEQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFP
input PDB
Selected Chain(s) A
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]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:00)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:59)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:30:27)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:30:28)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:30:28)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:30:29)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:30:30)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:30:30)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:30:31)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:30:32)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:30:32)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:30:33)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:30:34)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:30:34)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:30:35)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:30:45)
[INFO]       Movie:    Creting movie with webm format                                              (00:35:32)
[INFO]       Main:     Simulation completed successfully.                                          (00:35:39)
Show buried residues
Minimal score value
-3.7119
Maximal score value
2.1362
Average score
-0.5467
Total score value
-59.0399
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
257 K A 0.0000
258 P A 0.0000
259 R A -0.7268
260 Q A 0.0000
261 K A -0.5374
262 R A 0.0000
263 T A -1.0601
264 A A -1.4028
265 T A 0.0000
266 K A -2.1604
267 A A -0.7575
268 Y A -0.5276
269 N A -1.6866
270 V A 0.0000
271 T A -1.4783
272 Q A -1.5978
273 A A 0.0000
274 F A -0.6344
275 G A -1.2287
276 R A -2.5531
277 R A -2.1747
278 G A -1.7500
279 P A -1.9528
280 E A -2.3439
281 Q A -2.0251
282 T A -1.1266
283 Q A 0.0000
284 G A -0.0366
285 N A 0.0000
286 F A 0.0000
287 G A 0.0000
288 D A -1.8053
289 Q A -2.8063
290 E A -3.3610
291 L A 0.0000
292 I A -2.3695
293 R A -3.0108
294 Q A -2.5390
295 G A -2.3621
296 T A 0.0000
297 D A -2.5552
298 Y A -1.0856
299 K A -1.8017
300 H A -1.0700
301 W A 0.0000
302 P A -1.5661
303 Q A -1.5129
304 I A 0.0000
305 A A 0.0000
306 Q A -1.7115
307 F A 0.0000
308 A A 0.0000
309 P A 0.0000
310 S A -0.9876
311 A A 0.0954
312 S A 0.4056
313 A A 0.1148
314 F A 0.8073
315 F A 2.0459
316 G A 0.7236
317 M A 0.6439
318 S A 0.0619
319 R A 0.0122
320 I A 2.0403
321 G A 1.0168
322 M A 1.8339
323 E A 0.6814
324 V A 1.4769
325 T A 0.3527
326 P A -0.2423
327 S A -0.2067
328 G A -0.1279
329 T A 0.7549
330 W A 1.0292
331 L A 2.1362
332 T A 0.4805
333 Y A 0.8108
334 T A 0.0000
335 G A 0.0803
336 A A -0.1428
337 I A -0.1916
338 K A -1.7056
339 L A -1.3397
340 D A -2.5188
341 D A -3.3422
342 K A -3.7119
343 D A -3.4137
344 P A -2.3431
345 N A -2.0859
346 F A -0.9473
347 K A -1.2406
348 D A -0.7385
349 Q A 0.0000
350 V A 0.6671
351 I A 1.0949
352 L A 0.0000
353 L A 0.2702
354 N A -0.4901
355 K A -1.5828
356 H A 0.0000
357 I A 0.6740
358 D A 0.2878
359 A A 0.4267
360 Y A 0.7622
361 K A 0.3702
362 T A 0.9869
363 F A 1.8326
364 P A 0.6603
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, -0.5467 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_10 -0.5467 View CSV PDB
model_7 -0.6795 View CSV PDB
model_8 -0.6952 View CSV PDB
model_0 -0.706 View CSV PDB
model_4 -0.7206 View CSV PDB
model_11 -0.7583 View CSV PDB
model_9 -0.7593 View CSV PDB
model_1 -0.7988 View CSV PDB
model_5 -0.8225 View CSV PDB
model_6 -0.8528 View CSV PDB
model_2 -0.9021 View CSV PDB
model_3 -0.9228 View CSV PDB
input -0.9251 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018