Project name: rnasetdel

Status: done

Started: 2026-03-12 22:26:48
Chain sequence(s) A: MRPAALRGALLGCLCLALLCLGGADKRLRKHEWEKHGTCAAQVDALNSQKKYFGRSLELYRELDLNSVLLKLGIKPSINYYQVADFKDALARVYGVIPKIQCLPPSQDEEVQTIGQIELCLTKQDQQLQNCTEPGEQPSPKQEVWLANGAAESRGLRVCEDGPVFYPPPKKTKH
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations No
alphaCutter usage Used: no changes made
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]       PDB:      Running AlphaCutter                                                         (00:00:01)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:09)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:09)
[INFO]       CABS:     Running CABS flex simulation                                                (00:05:28)
[INFO]       Analysis: Starting Aggrescan4D on model_8.pdb                                         (00:35:54)
[INFO]       Analysis: Starting Aggrescan4D on model_6.pdb                                         (00:35:55)
[INFO]       Analysis: Starting Aggrescan4D on model_11.pdb                                        (00:35:55)
[INFO]       Analysis: Starting Aggrescan4D on model_7.pdb                                         (00:35:56)
[INFO]       Analysis: Starting Aggrescan4D on model_3.pdb                                         (00:35:57)
[INFO]       Analysis: Starting Aggrescan4D on model_5.pdb                                         (00:35:58)
[INFO]       Analysis: Starting Aggrescan4D on model_1.pdb                                         (00:35:58)
[INFO]       Analysis: Starting Aggrescan4D on model_0.pdb                                         (00:35:59)
[INFO]       Analysis: Starting Aggrescan4D on model_2.pdb                                         (00:36:00)
[INFO]       Analysis: Starting Aggrescan4D on model_4.pdb                                         (00:36:01)
[INFO]       Analysis: Starting Aggrescan4D on model_10.pdb                                        (00:36:01)
[INFO]       Analysis: Starting Aggrescan4D on model_9.pdb                                         (00:36:02)
[INFO]       Analysis: Starting Aggrescan4D on input.pdb                                           (00:36:03)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:36:06)
[INFO]       Main:     Simulation completed successfully.                                          (00:36:07)
Show buried residues
Minimal score value
-3.7992
Maximal score value
1.2806
Average score
-0.922
Total score value
-160.4273
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 M A 0.1074
2 R A -1.0141
3 P A -0.1793
4 A A 0.2161
5 A A 0.3784
6 L A 1.0444
7 R A -0.6165
8 G A -0.7866
9 A A -0.9019
10 L A 0.0000
11 L A 0.0000
12 G A -0.0120
13 C A -0.0680
14 L A 0.0000
15 C A 0.0000
16 L A 0.8335
17 A A 0.0000
18 L A 0.0000
19 L A 1.2413
20 C A 0.7384
21 L A 0.8289
22 G A -0.6050
23 G A -0.6380
24 A A -1.3736
25 D A -3.2907
26 K A -3.7209
27 R A -3.5382
28 L A -2.4215
29 R A -3.1477
30 K A -3.7992
31 H A -3.1987
32 E A -2.6324
33 W A 0.0000
34 E A -3.5201
35 K A -2.9902
36 H A 0.0000
37 G A -2.6201
38 T A -1.5687
39 C A -0.9155
40 A A 0.0000
41 A A -1.5847
42 Q A -2.5311
43 V A 0.0000
44 D A -3.0679
45 A A -2.0779
46 L A 0.0000
47 N A -3.0229
48 S A -2.4408
49 Q A -3.2193
50 K A -3.0728
51 K A -2.6580
52 Y A 0.0000
53 F A -1.2977
54 G A -1.3001
55 R A -2.1947
56 S A 0.0000
57 L A -0.8202
58 E A -2.4290
59 L A -2.1543
60 Y A -2.0887
61 R A -3.5188
62 E A -3.0810
63 L A 0.0000
64 D A -2.0821
65 L A 0.0000
66 N A -1.2540
67 S A -0.7215
68 V A -0.3535
69 L A 0.0000
70 L A 0.5587
71 K A -0.8694
72 L A -0.7119
73 G A -0.2662
74 I A -0.3307
75 K A -0.7350
76 P A 0.0000
77 S A 0.2964
78 I A 1.2062
79 N A 0.0918
80 Y A 1.2806
81 Y A 0.4780
82 Q A -1.3891
83 V A 0.0000
84 A A -1.7289
85 D A -1.2970
86 F A 0.0000
87 K A -1.7482
88 D A -2.1604
89 A A 0.0000
90 L A 0.0000
91 A A -1.0040
92 R A -1.8068
93 V A -0.7137
94 Y A 0.2255
95 G A -0.4149
96 V A 0.5570
97 I A 0.8063
98 P A 0.0041
99 K A -0.4904
100 I A 0.0000
101 Q A 0.0000
102 C A 0.0000
103 L A 0.0000
104 P A 0.0000
105 P A 0.0000
106 S A -1.2687
107 Q A 0.0000
108 D A -2.8144
109 E A -2.5747
110 E A -2.5178
111 V A 0.0000
112 Q A 0.0000
113 T A 0.0000
114 I A 0.0000
115 G A 0.0000
116 Q A -0.4467
117 I A 0.0000
118 E A 0.0000
119 L A 0.0000
120 C A -0.0661
121 L A 0.0000
122 T A -1.4140
123 K A -2.7831
124 Q A -2.6816
125 D A -2.0210
126 Q A -1.9898
127 Q A -1.7178
128 L A 0.0000
129 Q A -0.4219
130 N A 0.0000
131 C A 0.4941
132 T A -0.3323
133 E A -1.5978
134 P A -1.5978
135 G A -1.9196
136 E A -2.6544
137 Q A -2.2099
138 P A -1.6750
139 S A -1.2938
140 P A -0.9806
141 K A -0.9848
142 Q A 0.0000
143 E A -0.9960
144 V A 1.0910
145 W A 0.6121
146 L A -0.0966
147 A A -0.5971
148 N A -1.2547
149 G A -1.2688
150 A A -1.0164
151 A A -1.3950
152 E A -2.4299
153 S A -1.9281
154 R A -2.5587
155 G A -1.5972
156 L A 0.0000
157 R A 0.0000
158 V A -0.4368
159 C A 0.0000
160 E A -2.8607
161 D A -2.9257
162 G A 0.0000
163 P A -1.0404
164 V A 0.0000
165 F A 1.0859
166 Y A 0.0000
167 P A -0.0684
168 P A -0.8015
169 P A -1.2931
170 K A -2.2629
171 K A 0.0000
172 T A 0.0000
173 K A -1.7417
174 H A -1.8736
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, -0.922 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_5 -0.922 View CSV PDB
model_4 -0.9937 View CSV PDB
model_3 -1.0241 View CSV PDB
model_7 -1.0447 View CSV PDB
model_11 -1.0595 View CSV PDB
CABS_average -1.066 View CSV PDB
model_0 -1.068 View CSV PDB
model_10 -1.0818 View CSV PDB
model_9 -1.0851 View CSV PDB
model_1 -1.0884 View CSV PDB
model_6 -1.1241 View CSV PDB
model_8 -1.1313 View CSV PDB
model_2 -1.1696 View CSV PDB
input -1.1885 View CSV PDB