Project name: RBD_1hyk

Status: done

Started: 2026-06-12 13:29:21
Chain sequence(s) A: NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNNLFQSKPNVHVDGYFERLFRKSNLKPFERDISCVRLHESCLGQQVPCCDPCATCYCRFFNAFCYCRKLGTAMNPCSRTVVLSFELLHAPATVC
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                                         (00:25:01)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:25:02)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:25:03)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:25:03)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:25:04)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:25:05)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:25:05)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:25:06)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:25:07)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:25:07)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:25:08)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:25:09)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:25:10)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:25:13)
[INFO]       Main:     Simulation completed successfully.                                          (00:25:14)
Show buried residues
Minimal score value
-3.304
Maximal score value
2.7612
Average score
-0.4523
Total score value
-90.0153
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 -0.7931
2 L A -0.0682
3 C A -0.0753
4 P A -0.6789
5 F A 0.0000
6 G A -1.1652
7 E A -2.0339
8 V A 0.0000
9 F A -1.0630
10 N A -1.6478
11 A A 0.0000
12 T A -0.9024
13 R A -0.6069
14 F A -0.2364
15 A A -0.1377
16 S A 0.0000
17 V A 0.0000
18 Y A 0.0000
19 A A -0.1269
20 W A 0.0000
21 N A -0.8166
22 R A -1.2022
23 K A -1.3183
24 R A -2.0897
25 I A 0.0000
26 S A -0.6979
27 N A -1.0117
28 C A 0.1439
29 V A 1.1160
30 A A 0.0000
31 D A -2.1216
32 Y A 0.0000
33 S A -0.9493
34 V A -0.2821
35 L A 0.0000
36 Y A 0.0338
37 N A -0.5613
38 S A -0.4374
39 A A -0.4717
40 S A -0.7086
41 F A -0.5270
42 S A -0.5082
43 T A -0.2517
44 F A 0.1481
45 K A -0.3387
46 C A 0.4789
47 Y A 0.9358
48 G A -0.1117
49 V A 0.0000
50 S A -0.5587
51 P A -0.9604
52 T A -1.5047
53 K A -2.8184
54 L A 0.0000
55 N A -2.8103
56 D A -3.3040
57 L A 0.0000
58 C A -0.7008
59 F A 0.0000
60 T A -0.3874
61 N A -0.6903
62 V A 0.0000
63 Y A -0.7625
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 -1.3508
71 G A -1.9899
72 D A -2.8163
73 E A 0.0000
74 V A -1.5739
75 R A -2.8137
76 Q A -2.3722
77 I A 0.0000
78 A A -1.3793
79 P A -1.2246
80 G A -1.5211
81 Q A -1.6762
82 T A -1.7850
83 G A -1.7208
84 K A -2.3045
85 I A 0.0000
86 A A 0.0000
87 D A -1.3228
88 Y A 0.0000
89 N A 0.0000
90 Y A 0.0000
91 K A 0.0000
92 L A -0.1067
93 P A 0.0000
94 D A -1.4651
95 D A -1.7501
96 F A -0.3731
97 T A -0.0491
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 -0.8312
104 N A -1.6582
105 S A -1.5548
106 N A -1.7626
107 N A -0.8450
108 L A 0.7163
109 F A 0.1114
110 Q A -1.3838
111 S A -1.5712
112 K A -1.7672
113 P A -1.0574
114 N A -0.2927
115 V A 0.5817
116 H A -0.7232
117 V A 0.2781
118 D A 0.0615
119 G A 0.0000
120 Y A 0.0000
121 F A 0.0000
122 E A -0.7687
123 R A 0.0000
124 L A 1.0839
125 F A 1.2705
126 R A -1.3352
127 K A -2.1616
128 S A -1.6107
129 N A -1.4399
130 L A 0.5348
131 K A -0.6841
132 P A -0.0566
133 F A 0.4913
134 E A -0.1783
135 R A -0.8128
136 D A -0.3500
137 I A 1.2886
138 S A 0.6006
139 C A 0.4298
140 V A 0.0000
141 R A -1.4398
142 L A -1.0635
143 H A -1.3950
144 E A -1.6234
145 S A -0.4193
146 C A 0.0000
147 L A 1.1682
148 G A -0.3859
149 Q A -1.6065
150 Q A -1.3266
151 V A 0.1491
152 P A 0.0000
153 C A 0.0000
154 C A 0.0000
155 D A -0.7309
156 P A 0.0000
157 C A 0.0000
158 A A 0.0000
159 T A -0.8606
160 C A 0.0000
161 Y A -0.0170
162 C A 1.1110
163 R A 0.9929
164 F A 2.7612
165 F A 2.5707
166 N A 1.2678
167 A A 1.4265
168 F A 2.1974
169 C A 1.1699
170 Y A 0.2320
171 C A 0.0000
172 R A -1.8830
173 K A -2.2032
174 L A 0.0000
175 G A -1.3035
176 T A -0.6295
177 A A -0.6114
178 M A 0.0000
179 N A -1.4461
180 P A -0.8808
181 C A -0.6668
182 S A -0.9914
183 R A -1.2688
184 T A 0.0000
185 V A 0.0000
186 V A 0.0000
187 L A 0.0000
188 S A 0.0000
189 F A 0.0000
190 E A 0.0000
191 L A 0.0000
192 L A -0.1288
193 H A -0.7041
194 A A -0.4042
195 P A -0.3218
196 A A -0.2068
197 T A -0.1253
198 V A 0.0000
199 C A 0.1563
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, -0.4523 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 -0.4523 View CSV PDB
model_5 -0.5143 View CSV PDB
model_1 -0.5423 View CSV PDB
model_6 -0.5553 View CSV PDB
model_8 -0.5683 View CSV PDB
input -0.5828 View CSV PDB
CABS_average -0.5923 View CSV PDB
model_11 -0.5961 View CSV PDB
model_3 -0.6002 View CSV PDB
model_2 -0.6023 View CSV PDB
model_4 -0.6137 View CSV PDB
model_9 -0.6585 View CSV PDB
model_7 -0.6933 View CSV PDB
model_10 -0.7109 View CSV PDB