Project name: Notch3 EGF1-6_R75W Dynamic mode [mutate: RW36A]

Status: done

Started: 2025-02-26 04:10:50
Chain sequence(s) A: APPCLDGSPCANGGRCTQLPSREAACLCPPGWVGERCQLEDPCHSGPCAGRGVCQSSVVAGTARFSCRCPRGFRGPDCSLPDPCLSSPCAHGARCSVGPDGRFLCSCPPGYQGRSCRSDVDECRVGEPCRHGGTCLNTPGSFRCQCPAGYTGPLCENPAVPCAPSPCRNGGTCRQSGDLTYDCACLPGFEGQNCEVNVDDCPGHRCLNGGTCVDGVNTYNCQCPPEWTGQFCT
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage No
Dynamic mode Yes
Automated mutations No
Mutated residues RW36A
Energy difference between WT (input) and mutated protein (by FoldX) -0.226599 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                                                       (00:01:18)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:27)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:26:49)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:26:50)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:26:51)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:26:51)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:26:52)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:26:53)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:26:53)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:26:54)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:26:55)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:26:55)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:26:56)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:26:57)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:26:58)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:27:02)
[INFO]       Main:     Simulation completed successfully.                                          (00:27:03)
Show buried residues
Minimal score value
-3.0333
Maximal score value
1.733
Average score
-0.7019
Total score value
-163.5418
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 A A -0.3350
2 P A -0.9031
3 P A -0.7449
4 C A -0.8067
5 L A 0.0000
6 D A -2.0961
7 G A -1.4886
8 S A -1.3021
9 P A -1.5421
10 C A 0.0000
11 A A -0.5705
12 N A -1.0911
13 G A -1.0970
14 G A -1.1250
15 R A -1.6703
16 C A 0.0000
17 T A -0.8801
18 Q A -1.3963
19 L A -1.2278
20 P A -1.0955
21 S A -1.5594
22 R A -2.7256
23 E A -2.6572
24 A A 0.0000
25 A A -0.9219
26 C A -0.3220
27 L A 0.5556
28 C A -0.1559
29 P A -0.6111
30 P A -0.9008
31 G A -1.7761
32 W A 0.0000
33 V A -0.7943
34 G A -0.5706
35 E A -1.0007
36 W A -0.4697 mutated: RW36A
37 C A 0.0000
38 Q A -0.9680
39 L A 0.0000
40 E A -2.7866
41 D A -2.7376
42 P A -1.4777
43 C A -0.3470
44 H A -1.1127
45 S A -0.6534
46 G A -1.2945
47 P A -0.8251
48 C A 0.0000
49 A A -0.6256
50 G A -0.8766
51 R A -1.4414
52 G A -1.0724
53 V A -0.6654
54 C A -0.2997
55 Q A -0.4744
56 S A -0.4875
57 S A -0.3319
58 V A 0.0000
59 V A 0.9114
60 A A 0.3155
61 G A -0.4702
62 T A -0.3803
63 A A -1.0370
64 R A -1.1874
65 F A -0.4571
66 S A -0.5231
67 C A -1.0455
68 R A -2.0957
69 C A -1.7568
70 P A -1.4545
71 R A -2.0083
72 G A -0.6168
73 F A 0.7368
74 R A -0.8456
75 G A -0.5973
76 P A -1.0058
77 D A -1.4212
78 C A -0.4874
79 S A 0.0000
80 L A 0.8088
81 P A 0.0555
82 D A -0.4935
83 P A 0.0000
84 C A 0.1149
85 L A 0.7146
86 S A -0.0036
87 S A -0.5084
88 P A -1.0078
89 C A -1.3240
90 A A -1.2085
91 H A -1.4026
92 G A -1.3383
93 A A -1.2282
94 R A -1.3506
95 C A -0.0552
96 S A 0.0171
97 V A -0.1767
98 G A -0.8880
99 P A -1.5611
100 D A -2.3760
101 G A -1.6326
102 R A -1.3992
103 F A -0.0515
104 L A 1.0033
105 C A -0.0863
106 S A -0.4326
107 C A -0.9776
108 P A 0.0000
109 P A -0.8105
110 G A -1.3440
111 Y A 0.0000
112 Q A -2.9565
113 G A -2.8030
114 R A -2.4076
115 S A -1.6903
116 C A 0.0000
117 R A -3.0333
118 S A -2.8377
119 D A -2.7106
120 V A -1.8662
121 D A -1.3361
122 E A -1.4553
123 C A -1.3482
124 R A -1.6714
125 V A -1.1418
126 G A -1.5645
127 E A -2.4990
128 P A -1.4325
129 C A -1.8493
130 R A -2.3943
131 H A -1.6402
132 G A -1.3089
133 G A -0.7950
134 T A -0.6644
135 C A -0.5842
136 L A 0.1749
137 N A -0.7663
138 T A -0.5892
139 P A -0.7619
140 G A -0.8289
141 S A -0.7016
142 F A -1.2244
143 R A -1.5193
144 C A -0.9923
145 Q A -0.6578
146 C A -0.1599
147 P A 0.0033
148 A A 0.2333
149 G A 0.2728
150 Y A 0.0000
151 T A 0.0000
152 G A 0.0000
153 P A 0.2965
154 L A 0.3717
155 C A 0.0000
156 E A -1.1398
157 N A -0.9951
158 P A -0.6570
159 A A 0.1442
160 V A 0.9420
161 P A 0.7263
162 C A 0.6767
163 A A 0.3366
164 P A 0.0412
165 S A -0.5132
166 P A -0.9530
167 C A 0.0000
168 R A -1.8618
169 N A -0.8418
170 G A -0.8853
171 G A -1.1718
172 T A 0.0000
173 C A -1.1765
174 R A -2.4380
175 Q A -2.0734
176 S A -1.5189
177 G A -1.1807
178 D A -1.3303
179 L A 0.6140
180 T A -0.2466
181 Y A -0.8537
182 D A -1.6686
183 C A -0.5107
184 A A -0.2204
185 C A 0.1077
186 L A 0.7331
187 P A 0.8928
188 G A 1.0676
189 F A 1.1577
190 E A -0.8111
191 G A -1.4436
192 Q A -2.2055
193 N A -2.0332
194 C A -1.1497
195 E A 0.0000
196 V A -0.5930
197 N A 0.0000
198 V A 1.5597
199 D A 0.0000
200 D A -0.3621
201 C A 0.0000
202 P A -0.5853
203 G A -1.3964
204 H A -1.8981
205 R A -2.3002
206 C A 0.0000
207 L A -0.0641
208 N A -1.4569
209 G A -1.3456
210 G A -1.0747
211 T A 0.0000
212 C A -0.3337
213 V A 1.1431
214 D A 0.0000
215 G A 0.6151
216 V A 1.7314
217 N A 1.2706
218 T A 0.9542
219 Y A 1.7330
220 N A 0.3266
221 C A 0.0000
222 Q A -1.0777
223 C A 0.0000
224 P A -0.6726
225 P A -0.8394
226 E A -1.3201
227 W A 0.0142
228 T A -0.0298
229 G A -0.2414
230 Q A -0.7859
231 F A 0.8715
232 C A 0.0000
233 T A 0.0233
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, -0.7019 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_7 -0.7019 View CSV PDB
model_4 -0.7157 View CSV PDB
model_10 -0.7207 View CSV PDB
model_1 -0.7254 View CSV PDB
model_6 -0.7309 View CSV PDB
model_8 -0.7383 View CSV PDB
model_3 -0.7553 View CSV PDB
model_0 -0.759 View CSV PDB
CABS_average -0.7773 View CSV PDB
model_11 -0.8127 View CSV PDB
model_5 -0.8302 View CSV PDB
model_9 -0.9131 View CSV PDB
model_2 -0.9238 View CSV PDB
input -0.9668 View CSV PDB