Project name: RBD36_11B

Status: done

Started: 2026-06-15 15:37:16
Chain sequence(s) A: NLCPFGEVFNATRFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGVSPTKLNDLCFTNVYADSFVIRGDEVRQIAPGQTGKIADYNYKLPDDFTGCVIAWNSNEQVCTPGGEYAGKKIYVFRRHKLKPFERDTSKEAVISADDEKAKTEIALYKKETNAGLGFLEYDCRPATCPEEGDIYQVVVLSFELLHAPATVCGK
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                                         (00:36:56)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:36:57)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:36:58)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:36:59)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:37:00)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:37:01)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:37:01)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:37:02)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:37:03)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:37:04)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:37:05)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:37:05)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:37:06)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:37:10)
[INFO]       Main:     Simulation completed successfully.                                          (00:37:11)
Show buried residues
Minimal score value
-4.1966
Maximal score value
1.904
Average score
-0.704
Total score value
-142.2052
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 -0.8786
2 L A -0.2190
3 C A -0.1766
4 P A -0.7972
5 F A 0.0000
6 G A -1.3415
7 E A -2.1184
8 V A 0.0000
9 F A 0.0000
10 N A -1.8362
11 A A -1.3764
12 T A -1.0791
13 R A -1.2712
14 F A 0.0000
15 A A 0.0000
16 S A 0.0000
17 V A 0.0000
18 Y A 0.0000
19 A A -1.3091
20 W A 0.0000
21 N A -1.8062
22 R A -2.2588
23 K A -2.1446
24 R A -2.3793
25 I A 0.0000
26 S A -0.8295
27 N A -0.8279
28 C A 0.0000
29 V A 0.7124
30 A A 0.0000
31 D A -1.3169
32 Y A 0.0842
33 S A 0.5704
34 V A 0.0000
35 L A 0.0000
36 Y A 1.5716
37 N A 0.7975
38 S A 0.2746
39 A A 0.3663
40 S A 0.4255
41 F A 1.8817
42 S A 1.2578
43 T A 0.8189
44 F A 1.9040
45 K A 0.4895
46 C A 0.7340
47 Y A 1.0275
48 G A 0.1320
49 V A 0.0000
50 S A -0.5955
51 P A -0.4422
52 T A -1.2412
53 K A -2.5020
54 L A 0.0000
55 N A -1.9233
56 D A -2.7813
57 L A 0.0000
58 C A 0.4326
59 F A 0.0000
60 T A 0.0000
61 N A -0.7492
62 V A 0.0000
63 Y A -1.3496
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 -2.2880
71 G A 0.0000
72 D A -2.9344
73 E A 0.0000
74 V A 0.0000
75 R A -3.2645
76 Q A -3.0727
77 I A 0.0000
78 A A 0.0000
79 P A 0.0000
80 G A -0.7394
81 Q A -2.0837
82 T A -1.8064
83 G A 0.0000
84 K A -3.2008
85 I A 0.0000
86 A A 0.0000
87 D A -2.2692
88 Y A 0.0000
89 N A 0.0000
90 Y A -0.0745
91 K A -1.1358
92 L A 0.0000
93 P A 0.0000
94 D A -1.3244
95 D A -0.3490
96 F A 1.5881
97 T A 0.0000
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 0.0000
104 N A -0.5815
105 S A 0.0000
106 N A -2.1790
107 E A -2.6449
108 Q A -1.8859
109 V A 0.0000
110 C A 0.0000
111 T A -1.1661
112 P A -1.1100
113 G A -1.1267
114 G A -1.2679
115 E A -1.5318
116 Y A -0.1232
117 A A 0.0000
118 G A 0.0000
119 K A -1.1456
120 K A -1.3391
121 I A 0.0000
122 Y A -0.4717
123 V A 0.0000
124 F A -0.3604
125 R A 0.0000
126 R A -1.4741
127 H A -1.4673
128 K A -2.4013
129 L A -1.8273
130 K A -2.3291
131 P A -2.0267
132 F A 0.0000
133 E A -3.1200
134 R A 0.0000
135 D A -2.6271
136 T A -1.6622
137 S A -1.2667
138 K A -1.9880
139 E A 0.0000
140 A A -0.1678
141 V A 0.0000
142 I A 0.9349
143 S A 0.0000
144 A A -1.3396
145 D A -3.1692
146 D A -3.3489
147 E A -4.1966
148 K A -3.8136
149 A A 0.0000
150 K A -3.1385
151 T A -1.9399
152 E A -1.5652
153 I A -1.2645
154 A A -1.0108
155 L A -0.0808
156 Y A 0.0000
157 K A -2.3007
158 K A -2.1906
159 E A -1.3753
160 T A -1.0298
161 N A -1.4882
162 A A -1.4459
163 G A -1.0105
164 L A -0.8056
165 G A -0.5690
166 F A 0.0000
167 L A -0.3858
168 E A -1.4750
169 Y A 0.0000
170 D A -1.8203
171 C A 0.0000
172 R A -1.3090
173 P A -0.7445
174 A A -0.6841
175 T A -1.0773
176 C A -1.6891
177 P A -1.4646
178 E A -2.5178
179 E A -2.2647
180 G A -1.8585
181 D A -1.7317
182 I A 0.0000
183 Y A -1.0311
184 Q A 0.0000
185 V A 0.0000
186 V A 0.0000
187 V A 0.0000
188 L A 0.0000
189 S A 0.0000
190 F A 0.0000
191 E A 0.0000
192 L A 1.1281
193 L A 1.6772
194 H A -0.0209
195 A A -0.2217
196 P A -0.2736
197 A A -0.4284
198 T A -0.1278
199 V A 0.0000
200 C A 0.1346
201 G A -1.3393
202 K A -2.2152
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, -0.704 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_3 -0.704 View CSV PDB
model_4 -0.7065 View CSV PDB
model_6 -0.735 View CSV PDB
model_10 -0.74 View CSV PDB
model_0 -0.7715 View CSV PDB
model_8 -0.7836 View CSV PDB
CABS_average -0.7966 View CSV PDB
model_5 -0.7993 View CSV PDB
model_11 -0.8063 View CSV PDB
input -0.8188 View CSV PDB
model_1 -0.8516 View CSV PDB
model_9 -0.8568 View CSV PDB
model_7 -0.8631 View CSV PDB
model_2 -0.9411 View CSV PDB