Project name: Trail

Status: done

Started: 2026-07-17 10:45:00
Chain sequence(s) A: NNEESPTATVAEQGEDITSKKDRGVLKIVKRVGNGEETPMIGDKVYVHYKGKLSNGKKFDSSHDRNEPFVFSLGKGQVIKAWDIGVATMKKGEICHLLCKPEYAYGSAGSLPKIPSNATLFFEIELLDFKGE
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage No
Dynamic mode No
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-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:06)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/ea8dc28c2915269/tmp/folded.pdb                (00:02:06)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:42)
Show buried residues
Minimal score value
-3.7465
Maximal score value
1.749
Average score
-1.1478
Total score value
-151.5078
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
9 N A -2.6922
10 N A -3.1677
11 E A -3.7465
12 E A -3.2291
13 S A -1.7926
14 P A -1.2146
15 T A -1.0273
16 A A -1.2313
17 T A -1.3470
18 V A 0.0000
19 A A -1.6360
20 E A -2.6432
21 Q A -2.4855
22 G A -1.9174
23 E A -2.6003
24 D A -2.4587
25 I A -1.3173
26 T A 0.0000
27 S A -1.7946
28 K A -3.1207
29 K A -3.6802
30 D A -3.0420
31 R A -2.9822
32 G A 0.0000
33 V A 0.0000
34 L A 0.0000
35 K A 0.0000
36 I A -0.4943
37 V A 0.1181
38 K A -1.3919
39 R A -1.0148
40 V A 0.4374
41 G A -1.0417
42 N A -2.1474
43 G A -2.6335
44 E A -3.3446
45 E A -3.0421
46 T A -1.5060
47 P A 0.0000
48 M A 1.3204
49 I A 1.7490
50 G A -0.2733
51 D A -0.8371
52 K A -1.2415
53 V A 0.0000
54 Y A 0.0015
55 V A 0.0000
56 H A -1.3779
57 Y A -1.0162
58 K A -1.5280
59 G A 0.0000
60 K A -2.1946
61 L A 0.0000
62 S A -1.5254
63 N A -2.2116
64 G A -2.1914
65 K A -3.1967
66 K A -2.9807
67 F A -1.8046
68 D A -1.4707
69 S A -1.3223
70 S A -1.5525
71 H A -2.1817
72 D A -2.7692
73 R A -3.5507
74 N A -3.3358
75 E A -2.9475
76 P A -1.4703
77 F A -0.0599
78 V A 0.6734
79 F A 0.0000
80 S A -0.9533
81 L A 0.0000
82 G A -0.7772
83 K A -2.2483
84 G A -2.1899
85 Q A -2.0758
86 V A -1.1351
87 I A -1.0855
88 K A -2.1469
89 A A 0.0000
90 W A 0.0000
91 D A -0.7292
92 I A -0.1881
93 G A 0.0000
94 V A 0.0000
95 A A 0.2906
96 T A -0.2045
97 M A 0.0000
98 K A -2.1430
99 K A -1.9693
100 G A -0.9319
101 E A 0.0000
102 I A -0.4962
103 C A 0.0000
104 H A -0.4071
105 L A 0.0000
106 L A 0.0000
107 C A 0.0000
108 K A -1.5905
109 P A -1.6784
110 E A -2.3296
111 Y A -1.3701
112 A A -0.9504
113 Y A -0.3583
114 G A -1.1676
115 S A -1.0208
116 A A -0.0907
117 G A -0.2643
118 S A 0.0135
119 L A 0.6932
120 P A -0.2056
121 K A -1.7190
122 I A 0.0000
123 P A -0.5064
124 S A -0.6399
125 N A -1.8143
126 A A -1.2057
127 T A -0.9988
128 L A 0.0000
129 F A 0.0000
130 F A 0.0000
131 E A -0.7454
132 I A 0.0000
133 E A -1.1471
134 L A 0.0000
135 L A -0.1553
136 D A -0.9860
137 F A -1.1564
138 K A -2.0054
139 G A -1.6398
140 E A -2.5955
Download PDB file
View in 3Dmol

Calculations for various pH values

This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is globular. Max score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -1.1933 2.6276 View CSV PDB
4.5 -1.2639 2.6129 View CSV PDB
5.0 -1.3552 2.6016 View CSV PDB
5.5 -1.4448 2.6038 View CSV PDB
6.0 -1.5055 2.6337 View CSV PDB
6.5 -1.515 2.6982 View CSV PDB
7.0 -1.4703 2.7884 View CSV PDB
7.5 -1.3878 2.8912 View CSV PDB
8.0 -1.2858 2.9995 View CSV PDB
8.5 -1.1747 3.1116 View CSV PDB
9.0 -1.0587 3.2278 View CSV PDB