Project name: Barnase test run [mutate: YS90A, YS97A, YS24A]

Status: done

Started: 2025-03-04 00:44:27
Chain sequence(s) A: AQVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR
input PDB
Selected Chain(s) A
Distance of aggregation 5 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage Used: no changes made
Dynamic mode No
Automated mutations No
Mutated residues YS97A,YS24A,YS90A
Energy difference between WT (input) and mutated protein (by FoldX) -0.971369 kcal/mol
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.                                                               (00:00:26)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:26)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:26)
[INFO]       FoldX:    Building mutant model                                                       (00:02:56)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:04:14)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/e339324a8999b/tmp/folded.pdb                  (00:04:14)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:14)
Show buried residues
Minimal score value
-2.2417
Maximal score value
1.7882
Average score
-0.3368
Total score value
-37.0461
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 A A -0.1601
2 Q A -0.9810
3 V A 1.0441
4 I A 0.8894
5 N A -0.1293
6 T A -0.0319
7 F A -0.0683
8 D A -1.7138
9 G A -0.4171
10 V A 0.0000
11 A A 0.0000
12 D A -1.1418
13 Y A -0.0497
14 L A 0.0000
15 Q A -0.4736
16 T A 0.1135
17 Y A 1.1229
18 H A -1.0614
19 K A -1.8472
20 L A -0.1301
21 P A -0.3193
22 D A -1.8846
23 N A -0.8276
24 S A -0.0730 mutated: YS24A
25 I A 0.2357
26 T A -0.1643
27 K A -1.1215
28 S A -0.7010
29 E A -0.8973
30 A A 0.0000
31 Q A -1.2500
32 A A 0.0283
33 L A 1.4475
34 G A -0.2075
35 W A 0.0000
36 V A 1.7800
37 A A 0.1950
38 S A -0.4414
39 K A -1.3646
40 G A -0.4073
41 N A -1.5140
42 L A 0.0000
43 A A -0.3649
44 D A -1.8138
45 V A 0.3433
46 A A 0.0000
47 P A -0.3383
48 G A -0.5989
49 K A -0.5570
50 S A 0.0000
51 I A 0.0000
52 G A 0.0000
53 G A -0.1235
54 D A 0.0136
55 I A 1.6966
56 F A 0.0000
57 S A -0.2571
58 N A -0.6718
59 R A -2.2207
60 E A -2.2417
61 G A -1.0567
62 K A -1.3212
63 L A -0.0995
64 P A -0.1442
65 G A -0.7111
66 K A -1.8086
67 S A -0.6081
68 G A -0.8421
69 R A -1.9385
70 T A -0.3869
71 W A 0.0000
72 R A -0.8304
73 E A -0.3947
74 A A 0.0000
75 D A 0.0000
76 I A 0.0000
77 N A -0.7816
78 Y A -0.0016
79 T A -0.0816
80 S A -0.3111
81 G A -0.1508
82 F A 1.7882
83 R A 0.0048
84 N A -0.6281
85 S A -0.3532
86 D A -0.3307
87 R A 0.0000
88 I A 0.0000
89 L A 0.0000
90 S A 0.0000 mutated: YS90A
91 S A -0.0353
92 S A -0.5479
93 D A -1.7292
94 W A 0.2671
95 L A 0.3780
96 I A 0.0000
97 S A 0.0000 mutated: YS97A
98 K A -0.4208
99 T A 0.0000
100 T A -0.1764
101 D A -0.4551
102 H A -0.5861
103 Y A 0.0000
104 Q A -1.2061
105 T A -0.0992
106 F A 0.8735
107 T A -0.1875
108 K A -1.6234
109 I A -0.0196
110 R A -0.8339
Download PDB file
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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 -0.2998 4.0961 View CSV PDB
4.5 -0.3213 4.0961 View CSV PDB
5.0 -0.3462 4.0961 View CSV PDB
5.5 -0.3703 4.0961 View CSV PDB
6.0 -0.3893 4.0961 View CSV PDB
6.5 -0.3995 4.0961 View CSV PDB
7.0 -0.4002 4.0961 View CSV PDB
7.5 -0.3946 4.0961 View CSV PDB
8.0 -0.386 4.0961 View CSV PDB
8.5 -0.3746 4.0961 View CSV PDB
9.0 -0.3591 4.0961 View CSV PDB