Project name: Aggrescan My Fragment

Status: done

Started: 2020-11-18 00:35:49
Settings
Chain sequence(s) X: TDWNEIKGKVPVEVVQSPHSPNLYFVLLVPKVALEYHNLNNQVVKESLEVKATQSSFNPTQRLQKDSPVKDSSKQGEKLSETTASSMSSGMATSTRAKALKVEVERGSQSDSLLKNDFAKKPLKHKNSSGEVKLEAEKEFTEAWKPLLTTDQIAREKGMGATVVSFYDAPYSENHTAFGLVDHIDPKKMVENYPPSWKT
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                                                (00:04:52)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:53:27)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:53:28)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:53:29)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:53:30)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:53:32)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:53:33)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:53:34)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:53:36)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:53:37)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:53:38)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:53:40)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:53:41)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:53:43)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:53:45)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:53:45)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:53:45)
[INFO]       Main:     Simulation completed successfully.                                          (00:53:47)
Show buried residues
Minimal score value
-3.3004
Maximal score value
2.3468
Average score
-0.6133
Total score value
-122.0518
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 T X -1.0100
2 D X -2.2064
3 W X -1.3947
4 N X -2.8007
5 E X 0.0000
6 I X -1.4757
7 K X -2.7896
8 G X -1.9540
9 K X -1.4055
10 V X 0.3062
11 P X 0.4915
12 V X 1.4620
13 E X 0.0242
14 V X 1.5015
15 V X 1.4168
16 Q X -0.4039
17 S X -0.4621
18 P X -1.0219
19 H X -1.4834
20 S X -0.9535
21 P X -0.5908
22 N X -0.6297
23 L X 0.1407
24 Y X 1.0774
25 F X 1.7616
26 V X 1.6094
27 L X 1.2897
28 L X 0.0000
29 V X 0.8519
30 P X 0.0000
31 K X -1.5665
32 V X 0.0000
33 A X -0.6058
34 L X -0.3149
35 E X -1.3907
36 Y X 0.0000
37 H X -2.0773
38 N X -1.7250
39 L X -0.3663
40 N X -1.5176
41 N X -2.3317
42 Q X -2.2528
43 V X 0.0000
44 V X -0.7184
45 K X -1.2225
46 E X -0.5242
47 S X -0.2267
48 L X 0.5420
49 E X 0.1894
50 V X 0.6254
51 K X -1.2853
52 A X -1.2659
53 T X -1.2265
54 Q X -1.2848
55 S X -0.5119
56 S X 0.1458
57 F X 1.2347
58 N X -0.0191
59 P X -0.5716
60 T X -0.7036
61 Q X 0.0000
62 R X 0.0000
63 L X -0.2022
64 Q X -0.7593
65 K X 0.0000
66 D X -1.8391
67 S X -0.9781
68 P X 0.0000
69 V X 0.0000
70 K X 0.0000
71 D X -0.8359
72 S X -0.8259
73 S X -1.0087
74 K X -2.0705
75 Q X -2.5571
76 G X -1.8184
77 E X -1.9445
78 K X -1.8422
79 L X -0.2861
80 S X 0.0000
81 E X -0.3245
82 T X -0.7603
83 T X -0.9527
84 A X -0.7663
85 S X -0.5204
86 S X -0.0338
87 M X 0.4689
88 S X -0.0038
89 S X -0.3855
90 G X 0.0000
91 M X -0.0892
92 A X -0.2869
93 T X -0.0532
94 S X 0.0789
95 T X -0.4195
96 R X -0.9702
97 A X -0.8913
98 K X -1.6628
99 A X -0.2237
100 L X 1.0430
101 K X 0.6194
102 V X 1.7743
103 E X 0.1482
104 V X 0.3298
105 E X -1.5987
106 R X -2.0795
107 G X -1.4119
108 S X -0.9517
109 Q X -1.1753
110 S X -1.2686
111 D X -1.6132
112 S X -0.6879
113 L X 0.6357
114 L X 0.5886
115 K X -0.7276
116 N X -0.5438
117 D X 0.1145
118 F X 1.4607
119 A X 0.0000
120 K X -1.2977
121 K X -1.5110
122 P X 0.0000
123 L X -0.2734
124 K X -0.8971
125 H X 0.0000
126 K X -1.0884
127 N X -2.0307
128 S X -1.2929
129 S X -1.2996
130 G X -1.8485
131 E X -2.6708
132 V X 0.0000
133 K X -1.3353
134 L X -0.5732
135 E X -0.8025
136 A X -0.9059
137 E X -2.0329
138 K X -1.3611
139 E X -0.5739
140 F X 0.0005
141 T X -0.7318
142 E X -1.8825
143 A X -0.7870
144 W X -0.1013
145 K X -0.4494
146 P X 0.0851
147 L X -0.0835
148 L X -0.4578
149 T X -1.1222
150 T X -1.8917
151 D X -3.2191
152 Q X -2.9017
153 I X 0.0000
154 A X -2.5741
155 R X -3.3004
156 E X -2.4668
157 K X -1.9231
158 G X 0.0000
159 M X 0.0000
160 G X 0.0830
161 A X 0.5746
162 T X 0.0000
163 V X 0.8247
164 V X 0.0000
165 S X 1.6073
166 F X 1.9593
167 Y X 0.7649
168 D X -0.5080
169 A X -0.8552
170 P X -0.9854
171 Y X -0.2199
172 S X -1.0644
173 E X -2.5829
174 N X -2.3576
175 H X -1.8735
176 T X -0.4720
177 A X 0.9541
178 F X 2.3468
179 G X 1.6307
180 L X 1.5619
181 V X 0.0000
182 D X -1.2313
183 H X -0.8041
184 I X 0.4978
185 D X -0.9543
186 P X 0.0000
187 K X -2.8042
188 K X -2.4385
189 M X -1.2167
190 V X -1.5823
191 E X -2.9113
192 N X -2.1312
193 Y X -0.5364
194 P X -0.5190
195 P X -0.5164
196 S X -0.6292
197 W X 0.0000
198 K X -0.0684
199 T X -0.2639
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, -0.6133 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_9 -0.6133 View CSV PDB
model_0 -0.639 View CSV PDB
model_1 -0.6433 View CSV PDB
model_4 -0.6506 View CSV PDB
model_8 -0.6659 View CSV PDB
model_11 -0.6972 View CSV PDB
model_3 -0.6989 View CSV PDB
model_2 -0.7134 View CSV PDB
model_7 -0.7285 View CSV PDB
model_10 -0.7438 View CSV PDB
model_5 -0.7615 View CSV PDB
model_6 -0.8929 View CSV PDB
input -0.9618 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018