Project name: STT APR

Status: done

Started: 2021-02-26 14:34:49
Settings
Chain sequence(s) H: QVQLVQSGAEVKKPGSSVKVSCKASGGTFSTGAFTWVRQAPGQGLEWMGGIIPIFGTTNLAQNFQGRVTITADESTSTVYMELSSLRSEDTAVYYCARSSRIYDLNPSLTAYYDMDVWGQGTMVTVSS
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]                                                (00:00:01)
[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 all 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                                                (00:04:45)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (02:30:10)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (02:30:13)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (02:30:18)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (02:30:22)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (02:30:26)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (02:30:30)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (02:30:35)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (02:30:38)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (02:30:43)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (02:30:47)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (02:30:51)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (02:30:56)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (02:31:00)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (02:31:04)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (02:31:05)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (02:31:06)
[INFO]       Main:     Simulation completed successfully.                                          (02:31:10)
Show buried residues
Minimal score value
-2.9005
Maximal score value
2.8552
Average score
-0.4201
Total score value
-99.1414
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 -0.7518
2 V H -0.1611
3 Q H -0.7966
4 L H 0.0000
5 V H 0.8453
6 Q H 0.0000
7 S H -0.4057
8 G H -0.8531
9 A H -1.7018
10 E H -2.5754
11 V H 0.0000
12 K H -2.3177
13 K H 0.0000
14 P H -1.4013
15 G H -1.2283
16 S H -1.8328
17 S H -1.5669
18 V H -1.8187
19 K H -2.3086
20 V H 0.0000
21 S H -0.5740
22 C H 0.0000
23 K H -0.9970
24 A H -0.5676
25 S H -0.7978
26 G H -0.7571
27 G H -0.6567
28 T H -0.5672
29 F H 0.0000
30 S H -0.1180
31 T H 0.4919
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 0.0000
39 Q H 0.0000
40 A H -0.7103
41 P H -1.0759
42 G H -1.1282
43 Q H -1.0118
44 G H -0.7085
45 L H 0.0000
46 E H -0.7644
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 0.9243
54 I H 2.8552
55 F H 2.7447
56 G H 0.8075
57 T H 0.8522
58 T H 0.2491
59 N H 0.0000
60 L H 0.6607
61 A H 0.1798
62 Q H -0.6163
63 N H -1.3918
64 F H -0.9326
65 Q H -1.1726
66 G H -0.8496
67 R H 0.0000
68 V H 0.0000
69 T H -0.2713
70 I H 0.0000
71 T H -0.4555
72 A H -1.2124
73 D H -2.3066
74 E H -2.1314
75 S H -1.1865
76 T H -1.2028
77 S H 0.0000
78 T H -1.0371
79 V H 0.0000
80 Y H -0.4510
81 M H 0.0000
82 E H -1.3677
83 L H 0.0000
84 S H -1.1118
85 S H -0.8789
86 L H 0.0000
87 R H -2.0595
88 S H -1.5908
89 E H 0.0000
90 D H -1.8344
91 T H -0.8823
92 A H -0.2236
93 V H 0.0000
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 -0.4117
101 R H -0.6253
102 I H 0.5725
103 Y H -0.3595
104 D H -1.5197
105 L H -0.6564
106 N H -1.1838
107 P H -0.5326
108 S H 0.0000
109 L H 1.1121
110 T H 0.5202
111 A H 0.9072
112 Y H 0.0000
113 Y H 0.0000
114 D H 0.0000
115 M H 0.0000
116 D H 0.0000
117 V H 0.0000
118 W H -0.2742
119 G H 0.0000
120 Q H -0.2298
121 G H 0.1137
122 T H 0.0000
123 M H 0.5188
124 V H 0.0000
125 T H -0.8307
126 V H -1.2252
127 S H -1.3068
145 Q L -0.3892
146 S L 0.1410
147 V L 1.3275
148 L L 0.0000
149 T L -0.0215
150 Q L 0.0000
151 P L 0.0000
152 P L -0.9216
153 S L -0.9469
154 V L 0.0000
155 S L -0.3765
156 A L 0.0000
157 A L -0.5704
158 P L -0.8990
159 G L -1.2745
160 Q L -1.7088
161 K L -2.1105
162 V L 0.0000
163 T L -0.6847
164 I L 0.0000
165 S L -0.4583
166 C L 0.0000
167 S L -0.2355
168 G L -0.2033
169 S L 0.0673
170 S L 0.0676
171 S L -0.3517
172 D L -0.3803
173 I L 0.4636
174 G L -0.1758
175 N L 0.0000
176 N L -1.7290
177 Y L 0.0000
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 -0.2835
185 P L -0.5491
186 G L -0.1210
187 T L -0.1912
188 A L 0.0000
189 P L -0.1631
190 K L -0.6601
191 L L 0.0000
192 L L 0.0000
193 I L 0.0000
194 Y L 0.0000
195 D L 0.0000
196 N L -2.3552
197 N L -2.3576
198 K L -2.9005
199 R L -2.4604
200 P L -1.5065
201 S L -0.7942
202 G L -0.5197
203 I L 0.0720
204 P L -0.8143
205 D L -2.2033
206 R L -2.1063
207 F L 0.0000
208 S L -1.1924
209 G L -1.3065
210 S L -1.1335
211 K L -1.2138
212 S L -0.7966
213 G L -0.9411
214 T L -0.7189
215 S L -0.6755
216 A L 0.0000
217 T L -0.5797
218 L L 0.0000
219 G L -0.8730
220 I L 0.0000
221 T L -1.2877
222 G L -1.3251
223 L L -0.6502
224 Q L -0.9773
225 T L -0.4668
226 G L -0.5338
227 D L -1.0379
228 E L -1.9782
229 A L 0.0000
230 D L 0.0000
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 0.0416
238 S L 0.7154
239 S L 0.7020
240 L L 1.7546
241 S L 0.0000
242 A L 0.0000
243 W L 0.0000
244 V L 0.0000
245 F L 0.0000
246 G L -0.1701
247 G L -0.6212
248 G L -1.0804
249 T L 0.0000
250 K L -1.7796
251 L L 0.0000
252 T L -0.3813
253 V L 0.7714
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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, -0.4201 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_7 -0.4201 View CSV PDB
model_4 -0.4564 View CSV PDB
input -0.4577 View CSV PDB
model_11 -0.4617 View CSV PDB
model_2 -0.4678 View CSV PDB
model_1 -0.4729 View CSV PDB
model_3 -0.4809 View CSV PDB
model_8 -0.4913 View CSV PDB
model_9 -0.4939 View CSV PDB
model_0 -0.4981 View CSV PDB
model_10 -0.5287 View CSV PDB
model_5 -0.5473 View CSV PDB
model_6 -0.5754 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018