Project name: WFL APR

Status: done

Started: 2021-02-26 14:34:20
Settings
Chain sequence(s) H: QVQLVQSGAEVKKPGSSVKVSCKASGGTFWFGAFTWVRQAPGQGLEWMGGIIPIFGLTNLAQNFQGRVTITADESTSTVYMELSSLRSEDTAVYYCARSSRIYDLNPSLTAYYDMDVWGQGTMVTVSS
L: QSVLTQPPSVSAAPGQKVTISCSGSSSDIGNNYVSWYQQLPGTAPKLLIYDNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYYCGTWDSSLSAWVFGGGTKLTVL
input PDB
Selected Chain(s) H,L
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]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with all chain(s) selected           (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:02)
[INFO]       CABS:     Running CABS flex simulation                                                (00:04:53)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (02:36:12)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (02:36:16)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (02:36:20)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (02:36:24)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (02:36:28)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (02:36:32)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (02:36:36)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (02:36:40)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (02:36:44)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (02:36:49)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (02:36:53)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (02:36:57)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (02:37:02)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (02:37:07)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (02:37:07)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (02:37:07)
[INFO]       Main:     Simulation completed successfully.                                          (02:37:14)
Show buried residues
Minimal score value
-2.7234
Maximal score value
3.2552
Average score
-0.3386
Total score value
-79.9075
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
1 Q H -1.3345
2 V H 0.0000
3 Q H -0.9786
4 L H 0.0000
5 V H 0.1565
6 Q H 0.0000
7 S H -0.4152
8 G H -0.3243
9 A H 0.3015
10 E H 0.0957
11 V H 1.2861
12 K H 0.0000
13 K H -1.5047
14 P H -1.2912
15 G H -1.3419
16 S H -0.9078
17 S H -0.8365
18 V H 0.0000
19 K H -1.2819
20 V H 0.0000
21 S H -0.6114
22 C H 0.0000
23 K H -1.2092
24 A H 0.0000
25 S H -0.9590
26 G H -1.3171
27 G H -0.7230
28 T H -0.1506
29 F H 1.7589
30 W H 0.0000
31 F H 2.4039
32 G H 0.0000
33 A H 0.0000
34 F H 0.0000
35 T H 0.0000
36 W H 0.0000
37 V H 0.0000
38 R H -0.1449
39 Q H 0.0000
40 A H -0.9091
41 P H -1.4254
42 G H -1.3690
43 Q H -1.7396
44 G H -0.9718
45 L H 0.0000
46 E H -0.9947
47 W H 0.0000
48 M H 0.0000
49 G H 0.0000
50 G H 0.0000
51 I H 0.0000
52 I H 0.0000
53 P H 1.1834
54 I H 3.2552
55 F H 2.8489
56 G H 1.0331
57 L H 0.0000
58 T H 0.6189
59 N H 0.4409
60 L H 0.9729
61 A H -0.0697
62 Q H -1.7743
63 N H -2.4159
64 F H -2.0668
65 Q H -1.9555
66 G H -1.3726
67 R H -1.0240
68 V H -0.2197
69 T H 0.0145
70 I H 0.4947
71 T H -0.0184
72 A H -0.8396
73 D H -1.9017
74 E H -2.0201
75 S H -1.1414
76 T H -1.0975
77 S H 0.0000
78 T H -1.1403
79 V H 0.0000
80 Y H -0.2539
81 M H 0.0000
82 E H -0.8263
83 L H 0.0000
84 S H -0.9302
85 S H -0.9995
86 L H -1.3677
87 R H -2.3797
88 S H -1.8636
89 E H -1.8381
90 D H -2.0546
91 T H 0.0000
92 A H -0.0775
93 V H 0.2895
94 Y H 0.0000
95 Y H 0.0000
96 C H 0.0000
97 A H 0.0000
98 R H 0.0000
99 S H 0.0000
100 S H -0.3228
101 R H -0.4210
102 I H 0.1619
103 Y H 0.7635
104 D H 0.0000
105 L H 1.3680
106 N H 0.1117
107 P H -0.2411
108 S H 0.0584
109 L H 0.4320
110 T H 0.6422
111 A H 0.0000
112 Y H 0.0000
113 Y H 0.0000
114 D H 0.0000
115 M H 0.0000
116 D H -0.3104
117 V H 0.0000
118 W H 0.3770
119 G H -0.2129
120 Q H -0.6166
121 G H -0.5281
122 T H 0.0000
123 M H 0.8776
124 V H 0.0000
125 T H 0.6460
126 V H 0.3561
127 S H -0.8576
145 Q L -1.3418
146 S L 0.0898
147 V L 1.4788
148 L L 0.7121
149 T L 0.2419
150 Q L 0.0000
151 P L -0.5150
152 P L -0.4755
153 S L -0.6683
154 V L 0.1478
155 S L 0.1646
156 A L -0.1355
157 A L 0.0000
158 P L -0.9948
159 G L -1.5399
160 Q L -1.8866
161 K L -1.9107
162 V L -0.0892
163 T L 0.0000
164 I L 0.3533
165 S L -0.2828
166 C L 0.0000
167 S L -0.2206
168 G L 0.0302
169 S L -0.2190
170 S L -0.6768
171 S L -0.3322
172 D L 0.0239
173 I L 0.0000
174 G L -1.0798
175 N L -0.7755
176 N L -0.4508
177 Y L -0.2557
178 V L 0.0000
179 S L 0.0000
180 W L 0.0000
181 Y L 0.0000
182 Q L 0.0000
183 Q L 0.0000
184 L L 0.6809
185 P L -0.1259
186 G L -0.0983
187 T L 0.0074
188 A L 0.0000
189 P L -0.0275
190 K L -0.5196
191 L L 0.0000
192 L L 0.0000
193 I L 0.0000
194 Y L -1.3663
195 D L -1.6967
196 N L -2.1830
197 N L -2.3895
198 K L -2.7234
199 R L -1.9326
200 P L -1.2177
201 S L -0.5383
202 G L -0.7535
203 I L 0.0000
204 P L -0.7621
205 D L -1.1334
206 R L -1.1178
207 F L 0.0000
208 S L -0.8009
209 G L -0.7723
210 S L -1.0614
211 K L -1.4853
212 S L -1.0777
213 G L -1.0156
214 T L -0.9182
215 S L -0.7575
216 A L 0.0000
217 T L -0.3647
218 L L 0.0000
219 G L 0.0007
220 I L -0.0405
221 T L 0.0000
222 G L -1.1817
223 L L 0.0000
224 Q L -1.4921
225 T L -1.2443
226 G L -1.6890
227 D L -2.1116
228 E L 0.0000
229 A L -0.5970
230 D L -0.6931
231 Y L 0.0000
232 Y L 0.0000
233 C L 0.0000
234 G L 0.0000
235 T L 0.0000
236 W L 0.0000
237 D L 0.0000
238 S L 0.1917
239 S L 0.3806
240 L L 1.2432
241 S L 0.9110
242 A L 0.0000
243 W L 0.0000
244 V L 0.5458
245 F L 0.0000
246 G L -0.1411
247 G L -0.8651
248 G L -1.1007
249 T L 0.0000
250 K L -1.5005
251 L L 0.0000
252 T L 0.2311
253 V L 0.9556
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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, -0.3386 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_11 -0.3386 View CSV PDB
model_10 -0.3422 View CSV PDB
model_9 -0.3555 View CSV PDB
model_8 -0.3786 View CSV PDB
model_6 -0.4002 View CSV PDB
model_3 -0.4094 View CSV PDB
model_1 -0.4139 View CSV PDB
input -0.4185 View CSV PDB
model_7 -0.438 View CSV PDB
model_2 -0.4441 View CSV PDB
model_4 -0.4464 View CSV PDB
model_5 -0.4643 View CSV PDB
model_0 -0.554 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018