Project name: BAP1_WT [mutate: SC63A]

Status: done

Started: 2025-05-04 07:11:12
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 SC63A
Energy difference between WT (input) and mutated protein (by FoldX) 0.810354 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                                          (00:00:00)
[INFO]       FoldX:    Building mutant model                                                       (00:04:36)
[INFO]       CABS:     Running CABS flex simulation                                                (00:04:40)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:38:45)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:38:45)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:38:46)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:38:48)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:38:49)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:38:50)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:38:51)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:38:52)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:38:53)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:38:54)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:38:55)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:38:56)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:38:56)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:39:00)
[INFO]       Main:     Simulation completed successfully.                                          (00:39:01)
Show buried residues
Minimal score value
-2.4123
Maximal score value
1.8705
Average score
-0.2968
Total score value
-70.6491
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 0.2380
2 N A 0.0000
3 K A -1.7071
4 G A -0.3612
5 W A 1.2278
6 L A 0.7030
7 E A 0.0000
8 L A 0.0000
9 E A 0.0000
10 S A 0.0000
11 D A -0.3418
12 P A -0.1861
13 G A -0.3959
14 L A 0.2370
15 F A 0.0000
16 T A 0.0371
17 L A 0.3417
18 L A 0.0000
19 V A 0.0000
20 E A -1.9452
21 D A -1.2134
22 F A 0.0000
23 G A -0.4616
24 V A 0.0000
25 K A -1.7886
26 G A -0.7892
27 V A 0.0000
28 Q A -1.1983
29 V A 0.0000
30 E A -1.1966
31 E A -1.1461
32 I A 0.0000
33 Y A 0.9738
34 D A -1.5384
35 L A 0.0000
36 Q A -1.2179
37 S A -0.4567
38 K A -0.6826
39 C A 0.0000
40 Q A -0.5234
41 G A 0.0000
42 P A 0.0308
43 V A 0.3480
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 -0.4900
55 E A -0.8923
56 R A -1.1093
57 R A 0.0000
58 S A -0.6686
59 R A -1.9149
60 R A -0.9505
61 K A -1.7517
62 V A 0.0000
63 C A 0.2637 mutated: SC63A
64 T A -0.0163
65 L A 0.0000
66 V A 0.0000
67 D A -0.5724
68 D A -1.8401
69 T A -0.4435
70 S A -0.0456
71 V A 0.9096
72 I A 0.0000
73 D A -1.8912
74 D A -0.9109
75 D A -0.1288
76 I A 0.8491
77 V A 0.2089
78 N A -1.3324
79 N A -0.8395
80 M A 0.0000
81 F A 0.0000
82 F A 0.0000
83 A A 0.0000
84 H A -0.1923
85 Q A -0.2176
86 L A 0.1234
87 I A 0.0000
88 P A -0.1865
89 N A 0.0000
90 S A 0.0000
91 C A 0.0000
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 0.0000
102 N A 0.0000
103 C A 0.0000
104 S A -0.3860
105 S A -0.2524
106 V A 0.0000
107 D A -1.1622
108 L A 0.0000
109 G A -0.1978
110 P A -0.2963
111 T A 0.0000
112 L A 0.0000
113 S A -0.5499
114 R A -1.5902
115 M A 0.0000
116 K A -1.7832
117 D A -1.8428
118 F A 1.5996
119 T A -0.1367
120 K A -1.7524
121 G A -0.2180
122 F A 1.8705
123 S A 0.2570
124 P A -0.3809
125 E A -1.8465
126 S A -0.3146
127 K A 0.0000
128 G A 0.1644
129 Y A 1.2860
130 A A 0.0000
131 I A 0.0000
132 G A -0.5188
133 N A -0.3659
134 A A -0.1457
135 P A -0.3308
136 E A -0.6223
137 L A 0.0000
138 A A -0.3078
139 K A -1.8778
140 A A 0.0000
141 H A 0.0000
142 N A -1.4852
143 S A -0.3924
144 H A -0.1214
145 A A -0.1677
146 R A -1.0011
147 P A -0.4472
148 E A 0.0000
149 P A -0.2549
150 R A 0.0000
151 H A 0.0000
152 L A 0.3994
153 P A -0.0591
154 E A 0.0000
155 K A 0.0000
156 Q A -0.8035
157 N A -1.4110
158 G A -0.1915
159 L A 1.1660
160 S A 0.1920
161 A A 0.3989
162 V A 1.4243
163 R A -1.4979
164 T A 0.0000
165 M A 0.2289
166 E A 0.0000
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 0.2252
177 T A -0.0578
178 G A -0.3169
179 R A -0.7196
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 -0.8140
188 V A 0.1598
189 Y A 0.5096
190 P A 0.0000
191 I A 0.0000
192 D A -0.9415
193 H A -0.4473
194 G A -0.1894
195 P A 0.0978
196 W A 1.1276
197 G A -0.3426
198 E A -2.3715
199 D A -2.4008
200 E A -1.9871
201 E A 0.0000
202 W A 0.0000
203 T A -0.3369
204 D A -2.0120
205 K A -1.4884
206 A A 0.0000
207 R A -0.9299
208 R A -1.9519
209 V A 0.0000
210 I A 0.0000
211 M A 0.0330
212 E A -1.7289
213 R A 0.0000
214 I A 0.0000
215 G A -0.2827
216 L A 0.4851
217 A A 0.0000
218 T A -0.2082
219 A A 0.0188
220 G A -0.7940
221 E A -1.9613
222 P A -0.4565
223 Y A 1.2022
224 H A -0.3646
225 D A -1.1512
226 I A 0.0000
227 R A -1.5447
228 F A 0.0000
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 0.1055
235 P A 0.0000
236 D A -1.4250
237 R A -2.4123
238 R A -2.1992
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, -0.2968 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 -0.2968 View CSV PDB
model_9 -0.3052 View CSV PDB
model_1 -0.3117 View CSV PDB
model_4 -0.3133 View CSV PDB
model_2 -0.326 View CSV PDB
model_11 -0.3265 View CSV PDB
input -0.3269 View CSV PDB
model_5 -0.3278 View CSV PDB
CABS_average -0.3285 View CSV PDB
model_6 -0.3343 View CSV PDB
model_10 -0.3356 View CSV PDB
model_7 -0.3533 View CSV PDB
model_8 -0.3552 View CSV PDB
model_3 -0.356 View CSV PDB