Project name: simr

Status: done

Started: 2026-02-06 08:56:58
Chain sequence(s) H: QVQLQESGGGLVQPGGSLRLSCAASAYTISRNSMGWFRQAPGKGLEGVAAIESDGSTSYSDSVKGRFTISLDNSKNTLYLEMNSLRAEDTAVYYCAAPKVGLGPRTALGHLAFMTLPALNYWGQGTLVTVSS
input PDB
Selected Chain(s) H
Distance of aggregation 10 Å
FoldX usage No
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]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with H chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:03)
[INFO]       runJob:   FoldX not utilized. Treating input pdb file as it was already optimized.    (00:00:03)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:00:03)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/5b3c147c52da5ac/tmp/folded.pdb                (00:00:03)
[INFO]       Main:     Simulation completed successfully.                                          (00:00:59)
Show buried residues
Minimal score value
-2.9586
Maximal score value
2.2594
Average score
-0.4961
Total score value
-65.4858
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 Q H -1.5222
2 V H 0.0000
3 Q H -1.5883
4 L H 0.0000
5 Q H -1.4643
6 E H 0.0000
7 S H -0.7713
8 G H -0.8215
9 G H 0.1326
11 G H 0.8665
12 L H 1.4444
13 V H -0.1075
14 Q H -1.4596
15 P H -1.8674
16 G H -1.5546
17 G H -1.2436
18 S H -1.3502
19 L H -0.8983
20 R H -2.1441
21 L H 0.0000
22 S H -0.7759
23 C H 0.0000
24 A H -0.8666
25 A H -0.6277
26 S H -0.4584
27 A H 0.1292
28 Y H 0.4158
29 T H -0.4279
30 I H 0.0000
35 S H -1.5296
36 R H -2.4026
37 N H -1.4227
38 S H 0.0000
39 M H 0.0000
40 G H 0.0000
41 W H 0.0000
42 F H 0.0000
43 R H 0.0000
44 Q H -0.7023
45 A H 0.0000
46 P H -1.0693
47 G H -1.1867
48 K H -1.5764
49 G H -1.0119
50 L H -0.2374
51 E H -0.2930
52 G H 0.0000
53 V H 0.0000
54 A H 0.0000
55 A H 0.0000
56 I H 0.0000
57 E H -1.6527
58 S H -2.2420
59 D H -2.5293
63 G H -1.5024
64 S H -0.8776
65 T H -0.4330
66 S H -0.4433
67 Y H -0.7599
68 S H 0.0000
69 D H -2.5028
70 S H -1.8002
71 V H 0.0000
72 K H -2.5759
74 G H -1.7213
75 R H -1.5234
76 F H 0.0000
77 T H -0.8640
78 I H 0.0000
79 S H -0.1561
80 L H -0.4039
81 D H -1.1285
82 N H -1.5263
83 S H -1.4719
84 K H -2.1834
85 N H -1.2248
86 T H -0.9909
87 L H 0.0000
88 Y H -0.4326
89 L H 0.0000
90 E H -1.4228
91 M H 0.0000
92 N H -1.5008
93 S H -1.4134
94 L H 0.0000
95 R H -2.9586
96 A H -2.0096
97 E H -2.4918
98 D H 0.0000
99 T H -0.5082
100 A H 0.0000
101 V H 0.9078
102 Y H 0.0000
103 Y H 0.2123
104 C H 0.0000
105 A H 0.0000
106 A H 0.0000
107 P H -0.2720
108 K H -0.7559
109 V H 1.2244
110 G H 0.0118
111 L H 1.1238
111A G H -0.5384
111B P H -0.7974
111C R H -1.9482
111D T H -1.1666
111E A H -0.5162
111F L H -0.1006
112G G H 0.1680
112F H H 0.2956
112E L H 1.0601
112D A H 1.2695
112C F H 2.2594
112B M H 0.0000
112A T H 1.3442
112 L H 1.7206
113 P H 0.7850
114 A H 0.9249
115 L H 0.6508
116 N H -0.3354
117 Y H -0.6276
118 W H -0.1440
119 G H 0.0000
120 Q H -1.4152
121 G H -0.2047
122 T H 0.3641
123 L H 1.7810
124 V H 0.0000
125 T H 0.3072
126 V H 0.0000
127 S H -0.7629
128 S H -0.6670
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 -0.4246 5.1125 View CSV PDB
4.5 -0.4533 5.1156 View CSV PDB
5.0 -0.4836 5.1248 View CSV PDB
5.5 -0.5095 5.1484 View CSV PDB
6.0 -0.5244 5.1949 View CSV PDB
6.5 -0.5244 5.2557 View CSV PDB
7.0 -0.5128 5.3061 View CSV PDB
7.5 -0.4942 5.3335 View CSV PDB
8.0 -0.4706 5.3445 View CSV PDB
8.5 -0.4424 5.3483 View CSV PDB
9.0 -0.4108 5.3495 View CSV PDB