Project name: BAP1_WT [mutate: CG91A]

Status: done

Started: 2025-05-04 07:11:42
Chain sequence(s) A: MNKGWLELESDPGLFTLLVEDFGVKGVQVEEIYDLQSKCQGPVYGFIFLFKWIEERRSRRKVSTLVDDTSVIDDDIVNNMFFAHQLIPNSCATHALLSVLLNCSSVDLGPTLSRMKDFTKGFSPESKGYAIGNAPELAKAHNSHARPEPRHLPEKQNGLSAVRTMEAFHFVSYVPITGRLFELDGLKVYPIDHGPWGEDEEWTDKARRVIMERIGLATAGEPYHDIRFNLMAVVPDRR
input PDB
Selected Chain(s) A
Distance of aggregation 5 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
Dynamic mode Yes
Automated mutations No
Mutated residues CG91A
Energy difference between WT (input) and mutated protein (by FoldX) -3.76272 kcal/mol
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 minimization                                          (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:04:42)
[INFO]       CABS:     Running CABS flex simulation                                                (00:04:47)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:38:41)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:38:42)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:38:43)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:38:44)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:38:45)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:38:46)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:38:47)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:38:48)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:38:49)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:38:50)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:38:51)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:38:51)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:38:52)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:38:56)
[INFO]       Main:     Simulation completed successfully.                                          (00:38:57)
Show buried residues
Minimal score value
-2.2815
Maximal score value
1.9282
Average score
-0.279
Total score value
-66.3935
Download the table (csv)

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan4D score mutation
1 M A 0.8188
2 N A -1.2858
3 K A -1.4285
4 G A -0.5659
5 W A 0.3812
6 L A 0.4561
7 E A 0.0000
8 L A 0.0000
9 E A 0.0000
10 S A 0.0000
11 D A -0.6721
12 P A -0.2790
13 G A -0.3980
14 L A 0.4394
15 F A 0.0000
16 T A 0.2289
17 L A 1.1676
18 L A 0.0000
19 V A 0.0000
20 E A -1.8953
21 D A -1.4520
22 F A 0.0000
23 G A -0.2006
24 V A 0.3973
25 K A -1.3222
26 G A -0.5900
27 V A -0.1003
28 Q A -1.1269
29 V A -0.1706
30 E A -0.6912
31 E A -0.7474
32 I A 0.0000
33 Y A 0.9858
34 D A -1.5472
35 L A 0.0000
36 Q A -1.2220
37 S A -0.4323
38 K A -0.4386
39 C A 0.0000
40 Q A -0.4271
41 G A 0.0000
42 P A 0.0037
43 V A 0.1925
44 Y A 0.0000
45 G A 0.0000
46 F A 0.0000
47 I A 0.0000
48 F A 0.0000
49 L A 0.0000
50 F A 0.0000
51 K A 0.0000
52 W A 0.0000
53 I A 0.0000
54 E A -2.1141
55 E A -0.9711
56 R A -0.6128
57 R A -1.8705
58 S A -1.0382
59 R A -1.8762
60 R A 0.0000
61 K A -1.7225
62 V A 0.0000
63 S A -0.2171
64 T A -0.0078
65 L A 0.0000
66 V A 0.1824
67 D A -1.9533
68 D A -1.7454
69 T A -0.3129
70 S A 0.1003
71 V A 1.7878
72 I A 1.9282
73 D A -1.0770
74 D A -1.5106
75 D A -1.6847
76 I A 1.1596
77 V A 0.0000
78 N A -0.3797
79 N A -1.2996
80 M A 0.0000
81 F A 0.0000
82 F A 0.0000
83 A A 0.0000
84 H A 0.0000
85 Q A 0.0000
86 L A 0.0000
87 I A 0.3072
88 P A -0.0184
89 N A 0.0000
90 S A 0.0000
91 G A 0.0000 mutated: CG91A
92 A A 0.0000
93 T A 0.0000
94 H A 0.0000
95 A A 0.0000
96 L A 0.0000
97 L A 0.0000
98 S A 0.0000
99 V A 0.0000
100 L A 0.0000
101 L A 0.1953
102 N A -0.1707
103 C A 0.0000
104 S A -0.2169
105 S A -0.2145
106 V A 0.0000
107 D A -0.5570
108 L A 0.0000
109 G A -0.3954
110 P A -0.3667
111 T A 0.0000
112 L A 0.0000
113 S A -0.6352
114 R A -1.2525
115 M A 0.0000
116 K A -1.9942
117 D A -1.9902
118 F A 0.1453
119 T A -0.3831
120 K A -1.7910
121 G A -0.6261
122 F A 0.7486
123 S A 0.0348
124 P A -0.4171
125 E A -1.8433
126 S A -0.3079
127 K A 0.0000
128 G A 0.0399
129 Y A 1.2643
130 A A 0.2620
131 I A 0.0000
132 G A -0.1642
133 N A -1.2853
134 A A 0.0000
135 P A -0.2993
136 E A -0.4815
137 L A 0.0000
138 A A -0.3081
139 K A -1.8687
140 A A 0.0000
141 H A 0.0000
142 N A -1.5046
143 S A -0.4553
144 H A 0.0000
145 A A 0.0000
146 R A -0.5959
147 P A -0.3585
148 E A 0.0000
149 P A -0.1924
150 R A 0.0000
151 H A 0.0000
152 L A 0.4718
153 P A 0.0000
154 E A 0.0000
155 K A -0.6880
156 Q A -0.8339
157 N A -0.3504
158 G A -0.0338
159 L A 0.7078
160 S A 0.1286
161 A A 0.1036
162 V A 0.0008
163 R A -1.7845
164 T A -0.3155
165 M A 0.2681
166 E A -0.1382
167 A A 0.0000
168 F A 0.0000
169 H A 0.0000
170 F A 0.0000
171 V A 0.0000
172 S A 0.0000
173 Y A 0.0000
174 V A 0.0000
175 P A 0.0000
176 I A 0.3809
177 T A -0.0215
178 G A -0.5138
179 R A -1.2377
180 L A 0.0000
181 F A 0.0000
182 E A 0.0000
183 L A 0.0000
184 D A 0.0000
185 G A 0.0000
186 L A 0.0000
187 K A 0.0000
188 V A 0.4394
189 Y A 1.1344
190 P A 0.0000
191 I A 0.2943
192 D A -0.4328
193 H A -0.5608
194 G A -0.3886
195 P A 0.0022
196 W A 0.9878
197 G A -0.3982
198 E A -1.1571
199 D A -2.0740
200 E A -1.1740
201 E A -0.4323
202 W A 0.0000
203 T A -0.3723
204 D A -1.8414
205 K A -0.6060
206 A A 0.0000
207 R A -1.2408
208 R A -1.9369
209 V A 0.0000
210 I A 0.0000
211 M A 0.4676
212 E A -0.4378
213 R A 0.0000
214 I A 0.3879
215 G A -0.1567
216 L A 0.3363
217 A A 0.0000
218 T A -0.0088
219 A A -0.0741
220 G A -0.5198
221 E A -0.4118
222 P A 0.0605
223 Y A 0.9926
224 H A -0.9235
225 D A -1.0560
226 I A 0.0000
227 R A -0.5069
228 F A 0.1933
229 N A 0.0000
230 L A 0.0000
231 M A 0.0000
232 A A 0.0000
233 V A 0.0000
234 V A 0.0000
235 P A 0.0000
236 D A -1.8360
237 R A -2.2815
238 R A -2.1525
Download PDB file
View in 3Dmol

CABS-flex predictions of flexibility of input structure

In dynamic mode, A4D 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 A4D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A4D score, -0.279 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 A4D Score
model_0 -0.279 View CSV PDB
model_6 -0.2959 View CSV PDB
model_4 -0.3073 View CSV PDB
model_8 -0.3206 View CSV PDB
model_7 -0.3256 View CSV PDB
CABS_average -0.3269 View CSV PDB
model_10 -0.3304 View CSV PDB
input -0.3315 View CSV PDB
model_11 -0.3364 View CSV PDB
model_5 -0.3389 View CSV PDB
model_3 -0.3405 View CSV PDB
model_1 -0.3452 View CSV PDB
model_2 -0.3489 View CSV PDB
model_9 -0.3541 View CSV PDB