Project name: R36 WT_Dynamic

Status: done

Started: 2025-02-26 04:28:49
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
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]       CABS:     Running CABS flex simulation                                                (00:01:20)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:26:57)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:26:58)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:26:59)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:27:00)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:27:00)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:27:01)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:27:02)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:27:02)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:27:03)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:27:04)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:27:05)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:27:05)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:27:06)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:27:08)
[INFO]       Main:     Simulation completed successfully.                                          (00:27:10)
Show buried residues
Minimal score value
-3.0672
Maximal score value
1.3641
Average score
-0.8997
Total score value
-209.6247
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 -0.0890
2 P A -0.7428
3 P A -0.7974
4 C A -0.8804
5 L A -1.4703
6 D A -2.2414
7 G A -1.4993
8 S A -1.0861
9 P A -0.7785
10 C A -0.3011
11 A A -0.6668
12 N A -1.6905
13 G A -1.4809
14 G A -1.5107
15 R A -2.1714
16 C A -0.9834
17 T A -1.5431
18 Q A -2.1994
19 L A -1.5433
20 P A -1.5040
21 S A -1.5995
22 R A -2.7944
23 E A -2.9456
24 A A -2.1049
25 A A 0.0000
26 C A 0.0000
27 L A -1.2139
28 C A -1.0861
29 P A -0.7718
30 P A -0.9544
31 G A -1.2334
32 W A -1.0685
33 V A -1.1183
34 G A 0.0000
35 E A -2.1156
36 R A -1.7768
37 C A 0.0000
38 Q A -1.5156
39 L A 0.0000
40 E A -2.6859
41 D A -2.7815
42 P A -1.6258
43 C A -1.1751
44 H A -0.5013
45 S A -0.6098
46 G A -0.7466
47 P A -0.9534
48 C A -0.9454
49 A A -0.9139
50 G A -1.3601
51 R A -2.2572
52 G A -1.7259
53 V A -1.0244
54 C A -1.4085
55 Q A -1.5335
56 S A -1.1497
57 S A -0.8432
58 V A -1.0957
59 V A -0.5491
60 A A -1.2509
61 G A -1.5415
62 T A -0.7329
63 A A -1.2846
64 R A -1.3929
65 F A -0.7582
66 S A -1.2200
67 C A 0.0000
68 R A -2.1642
69 C A 0.0000
70 P A -1.2058
71 R A -1.4447
72 G A -0.6210
73 F A -0.0999
74 R A -1.3838
75 G A -1.5191
76 P A -1.8159
77 D A -1.8426
78 C A -1.4170
79 S A 0.0000
80 L A -0.8686
81 P A 0.0000
82 D A -0.6515
83 P A -0.0556
84 C A 0.3967
85 L A 0.5631
86 S A 0.1213
87 S A -0.6308
88 P A 0.0000
89 C A -0.4987
90 A A -0.6082
91 H A -0.8892
92 G A -1.0078
93 A A -1.2071
94 R A -1.5041
95 C A -0.3856
96 S A 0.2934
97 V A 0.1593
98 G A -0.4929
99 P A -1.4159
100 D A -2.6716
101 G A -2.2091
102 R A -2.0988
103 F A -0.2439
104 L A 0.8066
105 C A -0.0582
106 S A -0.7725
107 C A -0.8021
108 P A -0.8724
109 P A -0.2539
110 G A -0.7811
111 Y A 0.0000
112 Q A -2.5473
113 G A -2.4846
114 R A -2.7647
115 S A -1.2664
116 C A 0.0000
117 R A -2.7308
118 S A -2.5411
119 D A -3.0341
120 V A -1.6553
121 D A -0.8938
122 E A 0.0000
123 C A 0.0000
124 R A -1.8064
125 V A -0.3621
126 G A -1.0925
127 E A -2.1651
128 P A -1.6684
129 C A 0.0000
130 R A -2.9863
131 H A -2.2033
132 G A -1.5584
133 G A -1.5924
134 T A -1.4785
135 C A -1.2285
136 L A 0.2246
137 N A -0.0106
138 T A -0.1655
139 P A -0.7264
140 G A -0.2092
141 S A 0.2380
142 F A 0.4001
143 R A -0.8576
144 C A -1.3178
145 Q A -1.6396
146 C A 0.0000
147 P A -0.7762
148 A A -0.3617
149 G A 0.2402
150 Y A 0.8963
151 T A -0.0292
152 G A -0.2038
153 P A -0.3013
154 L A 0.1053
155 C A -1.3466
156 E A -1.5731
157 N A -0.9510
158 P A -0.0884
159 A A 0.5653
160 V A 1.3641
161 P A -0.3413
162 C A 0.0000
163 A A -0.1451
164 P A 0.1301
165 S A -0.0229
166 P A -0.3816
167 C A 0.0000
168 R A -0.7530
169 N A -0.7780
170 G A -0.9203
171 G A -1.1137
172 T A -0.7843
173 C A -1.4301
174 R A -3.0672
175 Q A -2.8083
176 S A -2.2142
177 G A -1.7170
178 D A -2.2637
179 L A -0.7365
180 T A -1.4743
181 Y A 0.0000
182 D A -2.6183
183 C A -1.5351
184 A A -0.4879
185 C A 0.1561
186 L A 0.2426
187 P A 0.2818
188 G A 0.3822
189 F A 1.2618
190 E A -1.1978
191 G A -1.6167
192 Q A -2.9245
193 N A -2.6897
194 C A -2.0509
195 E A -1.6081
196 V A -0.2818
197 N A -0.0801
198 V A 0.7191
199 D A -1.2243
200 D A 0.0000
201 C A 0.0000
202 P A -0.5252
203 G A -1.0573
204 H A -1.6094
205 R A -2.3336
206 C A 0.0000
207 L A 0.1167
208 N A -1.3753
209 G A -1.2481
210 G A -1.7220
211 T A -1.2447
212 C A -0.3706
213 V A 0.4071
214 D A 0.1083
215 G A 0.3576
216 V A 1.1819
217 N A 0.1637
218 T A 0.3724
219 Y A 0.6987
220 N A -0.5733
221 C A -0.4987
222 Q A -0.9958
223 C A -0.6833
224 P A 0.0000
225 P A -0.6598
226 E A -1.6243
227 W A -0.3085
228 T A -0.4664
229 G A -0.5418
230 Q A -0.4485
231 F A 0.2377
232 C A 0.0000
233 T A -0.6063
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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, -0.8997 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_9 -0.8997 View CSV PDB
model_10 -0.905 View CSV PDB
model_6 -0.9494 View CSV PDB
model_0 -0.9552 View CSV PDB
model_3 -0.9754 View CSV PDB
model_2 -0.9794 View CSV PDB
model_11 -0.9952 View CSV PDB
CABS_average -1.0021 View CSV PDB
model_4 -1.0054 View CSV PDB
input -1.0206 View CSV PDB
model_8 -1.0275 View CSV PDB
model_5 -1.0778 View CSV PDB
model_7 -1.0846 View CSV PDB
model_1 -1.1704 View CSV PDB