Project name: BAP1_WT [mutate: HQ169A]

Status: done

Started: 2025-05-04 07:12:22
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 HQ169A
Energy difference between WT (input) and mutated protein (by FoldX) -2.34647 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                                                       (00:04:47)
[INFO]       CABS:     Running CABS flex simulation                                                (00:04:57)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:39:13)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:39:14)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:39:15)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:39:15)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:39:16)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:39:17)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:39:18)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:39:19)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:39:19)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:39:20)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:39:21)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:39:22)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:39:23)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:39:26)
[INFO]       Main:     Simulation completed successfully.                                          (00:39:27)
Show buried residues
Minimal score value
-2.4574
Maximal score value
1.5734
Average score
-0.2914
Total score value
-69.3631
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 0.4816
2 N A -0.3896
3 K A -1.7989
4 G A -0.6526
5 W A 0.3638
6 L A 1.5734
7 E A 0.0000
8 L A 0.0000
9 E A 0.0000
10 S A 0.0000
11 D A -0.6190
12 P A -0.2130
13 G A -0.4036
14 L A 0.2854
15 F A 0.0000
16 T A 0.1271
17 L A 0.6307
18 L A 0.0000
19 V A 0.0000
20 E A -1.9136
21 D A -1.3496
22 F A 0.0000
23 G A -0.0810
24 V A 0.2409
25 K A -1.5991
26 G A -0.4064
27 V A 0.0000
28 Q A -1.1672
29 V A -0.1423
30 E A -0.8347
31 E A -1.9182
32 I A 0.0000
33 Y A 0.9741
34 D A -1.5097
35 L A -0.4176
36 Q A -1.2069
37 S A -0.6322
38 K A -1.1133
39 C A 0.0000
40 Q A -0.1379
41 G A 0.0000
42 P A 0.0255
43 V A 0.3022
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 -1.4761
55 E A -1.6367
56 R A 0.0000
57 R A -0.6209
58 S A -0.9388
59 R A -1.9139
60 R A -0.8711
61 K A -1.7101
62 V A -0.1189
63 S A -0.1655
64 T A 0.0000
65 L A 0.0000
66 V A 0.0000
67 D A -1.8685
68 D A -1.0065
69 T A -0.2131
70 S A 0.1564
71 V A 1.2684
72 I A 0.0000
73 D A -1.8944
74 D A -1.8558
75 D A -2.0090
76 I A 0.4164
77 V A 0.0000
78 N A -0.5508
79 N A -0.5871
80 M A 0.0000
81 F A 0.0000
82 F A 0.0000
83 A A 0.0000
84 H A -0.1684
85 Q A 0.0000
86 L A 0.0000
87 I A 0.9414
88 P A 0.0072
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 -0.1946
105 S A -0.1721
106 V A 0.0000
107 D A -0.4293
108 L A 0.0000
109 G A -0.1901
110 P A -0.2852
111 T A -0.0647
112 L A 0.0000
113 S A -0.5387
114 R A -2.0793
115 M A 0.0000
116 K A -0.9445
117 D A -1.8533
118 F A 1.0608
119 T A -0.3558
120 K A -1.7930
121 G A -0.7551
122 F A 0.0811
123 S A -0.0955
124 P A -0.4005
125 E A -1.8485
126 S A -0.4595
127 K A 0.0000
128 G A 0.0000
129 Y A 1.3185
130 A A 0.2733
131 I A 0.0000
132 G A 0.0000
133 N A -0.1598
134 A A -0.0691
135 P A -0.5487
136 E A -1.8124
137 L A 0.0000
138 A A -0.3086
139 K A -1.8738
140 A A -0.3153
141 H A 0.0000
142 N A -1.0914
143 S A -0.4377
144 H A -0.1398
145 A A -0.0034
146 R A 0.0000
147 P A -0.1661
148 E A -0.3166
149 P A -0.3400
150 R A -0.2490
151 H A 0.0000
152 L A 1.1233
153 P A -0.0728
154 E A 0.0000
155 K A -0.4077
156 Q A -1.2953
157 N A -0.4916
158 G A -0.0890
159 L A 0.4576
160 S A -0.1058
161 A A 0.3451
162 V A 1.4392
163 R A -1.5211
164 T A -0.3928
165 M A 0.0000
166 E A 0.0000
167 A A 0.0000
168 F A 0.0000
169 Q A 0.0000 mutated: HQ169A
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 0.5718
177 T A 0.0209
178 G A -0.2724
179 R A -0.8108
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 -0.1140
187 K A -1.3546
188 V A 0.7338
189 Y A 0.6940
190 P A 0.0000
191 I A 0.0000
192 D A 0.0000
193 H A -0.2656
194 G A -0.4204
195 P A -0.1770
196 W A 0.5348
197 G A -0.5736
198 E A -1.6753
199 D A -1.7786
200 E A -1.4444
201 E A -0.7037
202 W A 0.0000
203 T A -0.2982
204 D A -1.3997
205 K A -1.1576
206 A A 0.0000
207 R A -0.6747
208 R A -1.6588
209 V A -0.2487
210 I A 0.0000
211 M A -0.0017
212 E A -1.5189
213 R A 0.0000
214 I A 0.3571
215 G A -0.0239
216 L A 0.3144
217 A A 0.0000
218 T A -0.0504
219 A A -0.0497
220 G A -0.4579
221 E A 0.0000
222 P A -0.0029
223 Y A 1.0318
224 H A -0.8167
225 D A -0.4643
226 I A 0.0000
227 R A -0.3546
228 F A 0.2545
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 0.1782
235 P A 0.0000
236 D A -1.7490
237 R A -2.4574
238 R A -2.1928
Download PDB file
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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, -0.2914 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_5 -0.2914 View CSV PDB
model_11 -0.2979 View CSV PDB
model_1 -0.2999 View CSV PDB
model_8 -0.3007 View CSV PDB
model_2 -0.301 View CSV PDB
model_10 -0.305 View CSV PDB
CABS_average -0.3121 View CSV PDB
model_4 -0.3123 View CSV PDB
model_0 -0.3129 View CSV PDB
model_3 -0.3145 View CSV PDB
model_6 -0.322 View CSV PDB
model_7 -0.3281 View CSV PDB
input -0.3316 View CSV PDB
model_9 -0.36 View CSV PDB