Project name: R4mu_2

Status: done

Started: 2026-02-28 20:09:19
Chain sequence(s) A: SMLESLVGKISLLLTQVRLTGQNIDDLYADLVAGYEAGTLGQIETYRNQLIQLLAQLLMLLDELLRLIRELMRYVKENNVSENLLIILEEMLTALDEYKWIFQQANALFTQLLIGLATGTLTQEQLDAIIAQLEALRKLGEQVSTKIDSLMNKIKEELYE
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                                          (00:04:14)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/f7b7a775b60f5ed/tmp/folded.pdb                (00:04:14)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:24)
Show buried residues
Minimal score value
-3.9209
Maximal score value
0.797
Average score
-1.0597
Total score value
-169.5441
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 S A -0.5012
2 M A 0.0389
3 L A -0.3817
4 E A -1.8978
5 S A -1.2876
6 L A 0.0000
7 V A 0.0000
8 G A -1.0716
9 K A -1.1838
10 I A 0.0000
11 S A -0.1227
12 L A 0.7970
13 L A 0.0000
14 L A -0.0681
15 T A -0.0284
16 Q A -0.2775
17 V A 0.0000
18 R A -1.4494
19 L A -0.5328
20 T A 0.0000
21 G A 0.0000
22 Q A -2.2862
23 N A -2.4922
24 I A 0.0000
25 D A -2.3631
26 D A -3.1808
27 L A 0.0000
28 Y A 0.0000
29 A A -1.7146
30 D A -2.1692
31 L A 0.0000
32 V A -0.8145
33 A A -1.0313
34 G A -1.0903
35 Y A -1.0905
36 E A -1.8690
37 A A -0.9342
38 G A -0.9494
39 T A -0.6374
40 L A -0.6346
41 G A -0.9458
42 Q A -1.4668
43 I A 0.0000
44 E A -2.5562
45 T A -1.9494
46 Y A 0.0000
47 R A -1.8146
48 N A -2.3076
49 Q A -1.9875
50 L A 0.0000
51 I A -0.4807
52 Q A -1.4371
53 L A -0.7904
54 L A 0.0000
55 A A -0.1805
56 Q A -0.2315
57 L A 0.0000
58 L A -0.0225
59 M A 0.3255
60 L A -0.3555
61 L A 0.0000
62 D A -2.1856
63 E A -1.6595
64 L A 0.0000
65 L A -2.2881
66 R A -3.0073
67 L A 0.0000
68 I A 0.0000
69 R A -3.4558
70 E A -2.7116
71 L A 0.0000
72 M A 0.0000
73 R A -3.7861
74 Y A -2.4551
75 V A 0.0000
76 K A -3.9209
77 E A -3.7539
78 N A -2.8884
79 N A -2.9328
80 V A -1.2130
81 S A -1.3587
82 E A -2.0295
83 N A -1.1387
84 L A 0.0000
85 L A -0.9678
86 I A 0.3440
87 I A 0.0000
88 L A 0.0000
89 E A -2.1217
90 E A -2.3865
91 M A 0.0000
92 L A -1.9326
93 T A -1.9779
94 A A 0.0000
95 L A 0.0000
96 D A -2.5071
97 E A -1.6697
98 Y A 0.0000
99 K A -1.3335
100 W A -0.5272
101 I A 0.0000
102 F A 0.0000
103 Q A -1.2268
104 Q A -0.9310
105 A A 0.0000
106 N A -0.5625
107 A A -0.6150
108 L A -0.3693
109 F A 0.0000
110 T A -0.0493
111 Q A -0.3279
112 L A 0.0000
113 L A 0.0000
114 I A 0.3277
115 G A 0.0000
116 L A 0.0139
117 A A -0.2546
118 T A 0.0568
119 G A -0.3713
120 T A -0.2346
121 L A -0.8136
122 T A -1.6149
123 Q A -2.6029
124 E A -3.1153
125 Q A -2.3947
126 L A 0.0000
127 D A -2.4314
128 A A -1.5751
129 I A -1.1270
130 I A 0.0000
131 A A -0.9848
132 Q A -1.1665
133 L A 0.0000
134 E A -1.7432
135 A A -1.2956
136 L A 0.0000
137 R A -2.4035
138 K A -2.8500
139 L A -1.6505
140 G A 0.0000
141 E A -2.9809
142 Q A -2.5679
143 V A 0.0000
144 S A -1.9437
145 T A -1.5817
146 K A -1.9841
147 I A 0.0000
148 D A -1.5684
149 S A -1.4242
150 L A 0.0000
151 M A 0.0000
152 N A -2.8857
153 K A -3.0204
154 I A 0.0000
155 K A -2.8816
156 E A -3.5737
157 E A -2.5787
158 L A -1.3748
159 Y A -1.1302
160 E A -2.4456
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 -0.6458 2.1999 View CSV PDB
4.5 -0.7409 1.9866 View CSV PDB
5.0 -0.869 1.7671 View CSV PDB
5.5 -1.01 1.5851 View CSV PDB
6.0 -1.1407 1.4149 View CSV PDB
6.5 -1.2417 1.2756 View CSV PDB
7.0 -1.3039 1.174 View CSV PDB
7.5 -1.3327 1.1025 View CSV PDB
8.0 -1.3411 1.0486 View CSV PDB
8.5 -1.3373 1.1418 View CSV PDB
9.0 -1.3227 1.2667 View CSV PDB