Project name: RBD16_10A

Status: done

Started: 2026-06-15 15:36:58
Chain sequence(s) A: NLCPFGEVFNATRFASVYAWNRKRISNCIADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLSVAEQPYVNLFRKSNLKPFERDISVEPLVEETYTYNAATGKWTQKVTNGSPKTVTLPNDNPAISDFYRVVVLSFELLPAPPTVCGP
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage No
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]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       runJob:   FoldX not utilized. Treating input pdb file as it was already optimized.    (00:00:01)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:35:33)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:35:34)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:35:35)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:35:36)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:35:37)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:35:38)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:35:39)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:35:40)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:35:41)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:35:42)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:35:43)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:35:44)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:35:44)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:35:50)
[INFO]       Main:     Simulation completed successfully.                                          (00:35:51)
Show buried residues
Minimal score value
-2.7247
Maximal score value
1.8225
Average score
-0.4906
Total score value
-95.1746
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 N A -0.7978
2 L A 0.0000
3 C A -0.1074
4 P A -0.4945
5 F A 0.0000
6 G A -0.9265
7 E A -1.3276
8 V A 0.0000
9 F A 0.0000
10 N A -1.0937
11 A A -0.5760
12 T A -1.3103
13 R A -1.9281
14 F A -0.6234
15 A A -0.5628
16 S A -0.1314
17 V A 0.0000
18 Y A 0.0000
19 A A -0.3415
20 W A 0.0000
21 N A -1.9620
22 R A -2.3115
23 K A -2.1176
24 R A -2.3914
25 I A 0.0000
26 S A -1.0927
27 N A -1.0345
28 C A 0.0000
29 I A 0.6175
30 A A 0.0000
31 D A -0.3999
32 Y A -0.1973
33 S A -0.1441
34 V A -0.0830
35 L A 0.0000
36 Y A -0.2460
37 N A -1.2779
38 S A -0.8295
39 A A -0.3730
40 S A -0.3243
41 F A 0.1075
42 S A -0.3711
43 T A -0.1248
44 F A 0.6656
45 K A -0.2236
46 C A 0.5138
47 Y A 1.2790
48 G A 0.4293
49 V A 0.0000
50 S A -0.7168
51 P A -1.0339
52 T A -1.6243
53 K A -2.5002
54 L A 0.0000
55 N A -1.8932
56 D A -2.6077
57 L A 0.0000
58 C A -0.1605
59 F A 0.0000
60 T A 0.0000
61 N A -1.2435
62 V A 0.0000
63 Y A -0.9769
64 A A 0.0000
65 D A 0.0000
66 S A 0.0000
67 F A 0.0000
68 V A 0.0000
69 I A 0.0000
70 R A -0.8523
71 G A 0.0000
72 D A -1.5559
73 E A 0.0000
74 V A 0.0000
75 R A -2.3793
76 Q A -1.8379
77 I A -1.0096
78 A A -0.8381
79 P A -1.0780
80 G A -1.3154
81 Q A -1.4744
82 T A -1.1046
83 G A -0.7763
84 K A -0.3499
85 I A 0.0000
86 A A 0.0000
87 D A 0.0000
88 Y A 0.0000
89 N A 0.0000
90 Y A -0.1108
91 K A 0.0000
92 L A 0.0000
93 P A -0.2334
94 D A -1.0956
95 D A 0.1012
96 F A 1.5858
97 T A 1.0402
98 G A 0.0000
99 C A 0.0000
100 V A 0.0000
101 I A 0.0000
102 A A 0.0000
103 W A -0.1718
104 N A -0.7914
105 S A -0.6708
106 N A -1.2636
107 N A -1.0972
108 L A 0.2024
109 S A 0.0000
110 V A -0.6046
111 A A -0.6567
112 E A -1.6044
113 Q A -1.0451
114 P A -0.7259
115 Y A 0.0000
116 V A 0.1345
117 N A 0.0000
118 L A 0.0000
119 F A 0.1715
120 R A -0.7542
121 K A -1.9653
122 S A -1.2700
123 N A -1.3671
124 L A 0.0878
125 K A -0.1925
126 P A 0.0000
127 F A 0.3832
128 E A -1.4603
129 R A -2.4824
130 D A -1.6838
131 I A 1.0267
132 S A 0.0000
133 V A 1.8225
134 E A 0.3232
135 P A 0.0871
136 L A 0.8049
137 V A 0.0596
138 E A -0.2730
139 E A 0.0000
140 T A -0.3999
141 Y A 0.0000
142 T A -0.8519
143 Y A 0.0000
144 N A -1.2164
145 A A -1.1611
146 A A -0.7061
147 T A -0.8747
148 G A -1.5735
149 K A -1.7783
150 W A 0.0000
151 T A -0.5443
152 Q A -0.6986
153 K A -1.4797
154 V A -1.1507
155 T A -1.2615
156 N A -1.5209
157 G A -1.2361
158 S A -1.4062
159 P A -1.6719
160 K A -2.0626
161 T A -0.6311
162 V A 0.7391
163 T A 0.1316
164 L A -0.0593
165 P A -1.1338
166 N A 0.0000
167 D A -2.7247
168 N A -2.2887
169 P A -1.5282
170 A A -1.1820
171 I A -0.8888
172 S A -1.4212
173 D A -1.3283
174 F A 0.0000
175 Y A 0.0000
176 R A 0.0000
177 V A 0.0000
178 V A 0.0000
179 V A 0.0000
180 L A 0.0000
181 S A 0.0000
182 F A 0.0000
183 E A 0.7925
184 L A 1.6672
185 L A 0.5073
186 P A -0.0240
187 A A 0.3219
188 P A -0.0220
189 P A -0.2510
190 T A -0.4153
191 V A 0.0000
192 C A -0.1925
193 G A 0.0000
194 P A -0.5184
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, -0.4906 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_10 -0.4906 View CSV PDB
model_11 -0.5121 View CSV PDB
model_4 -0.5446 View CSV PDB
model_7 -0.5538 View CSV PDB
input -0.554 View CSV PDB
model_1 -0.5627 View CSV PDB
model_6 -0.5638 View CSV PDB
model_2 -0.5663 View CSV PDB
CABS_average -0.5732 View CSV PDB
model_0 -0.5749 View CSV PDB
model_5 -0.5877 View CSV PDB
model_9 -0.6148 View CSV PDB
model_8 -0.6229 View CSV PDB
model_3 -0.6839 View CSV PDB