Project name: Barnase test run [mutate: YS90A, YS97A, YS24A] [mutate: SY90A, SY97A, SY24A]

Status: done

Started: 2025-03-04 00:55:21
Chain sequence(s) A: AQVINTFDGVADYLQTYHKLPDNSITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILSSSDWLISKTTDHYQTFTKIR
input PDB
Selected Chain(s) A
Distance of aggregation 5 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage No
Dynamic mode No
Automated mutations No
Mutated residues SY97A,SY24A,SY90A
Energy difference between WT (input) and mutated protein (by FoldX) 8.94524 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure
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]       FoldX:    Building mutant model                                                       (00:00:56)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:05)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/9eb447864e684d8/tmp/folded.pdb                (00:02:05)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:04)
Show buried residues
Minimal score value
-2.2417
Maximal score value
1.7888
Average score
-0.3318
Total score value
-36.494
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 -0.9422
3 V A 1.2553
4 I A 0.9227
5 N A -0.1204
6 T A -0.0310
7 F A -0.0821
8 D A -1.7607
9 G A -0.4255
10 V A 0.0000
11 A A 0.0000
12 D A -1.2298
13 Y A -0.0609
14 L A 0.0000
15 Q A -0.4777
16 T A 0.1171
17 Y A 1.1236
18 H A -1.0614
19 K A -1.8812
20 L A 0.0000
21 P A 0.0000
22 D A -1.8781
23 N A -0.8124
24 Y A 0.0000 mutated: SY24A
25 I A 0.2418
26 T A -0.1707
27 K A -1.1559
28 S A -0.7089
29 E A -0.9063
30 A A 0.0000
31 Q A -1.2523
32 A A 0.0288
33 L A 1.4516
34 G A -0.2265
35 W A 0.0000
36 V A 1.7809
37 A A 0.2006
38 S A -0.4393
39 K A -1.3577
40 G A -0.3673
41 N A -1.2911
42 L A 0.0000
43 A A -0.3649
44 D A -1.7694
45 V A 0.4443
46 A A 0.0000
47 P A -0.3383
48 G A -0.6017
49 K A -0.5720
50 S A 0.0000
51 I A 0.0000
52 G A 0.0000
53 G A -0.2247
54 D A -0.1008
55 I A 1.1554
56 F A 0.0000
57 S A -0.2569
58 N A -0.6705
59 R A -2.2205
60 E A -2.2417
61 G A -1.0122
62 K A -1.0767
63 L A -0.0588
64 P A -0.2202
65 G A -0.8039
66 K A -1.8234
67 S A -0.6081
68 G A -0.8421
69 R A -1.9375
70 T A -0.3817
71 W A 0.0000
72 R A -0.7184
73 E A -0.3586
74 A A 0.0000
75 D A 0.0000
76 I A 0.0000
77 N A -0.7805
78 Y A -0.0016
79 T A -0.0816
80 S A -0.3111
81 G A -0.1508
82 F A 1.7888
83 R A 0.0104
84 N A -0.6241
85 S A -0.3535
86 D A -0.3352
87 R A 0.0000
88 I A 0.0000
89 L A 0.0000
90 Y A 0.1369 mutated: SY90A
91 S A -0.0065
92 S A -0.5172
93 D A -1.5774
94 W A 0.2451
95 L A 0.3411
96 I A 0.0000
97 Y A -0.1527 mutated: SY97A
98 K A -0.3789
99 T A 0.0000
100 T A -0.1777
101 D A -0.4598
102 H A -0.5920
103 Y A 0.0000
104 Q A -1.2059
105 T A -0.1209
106 F A 0.7497
107 T A -0.1926
108 K A -1.6247
109 I A -0.1006
110 R A -0.7403
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 -0.304 4.0982 View CSV PDB
4.5 -0.3275 4.0982 View CSV PDB
5.0 -0.3531 4.0982 View CSV PDB
5.5 -0.3772 4.0982 View CSV PDB
6.0 -0.3955 4.0982 View CSV PDB
6.5 -0.4043 4.0982 View CSV PDB
7.0 -0.4034 4.0982 View CSV PDB
7.5 -0.3964 4.0982 View CSV PDB
8.0 -0.3862 4.0982 View CSV PDB
8.5 -0.3725 4.0982 View CSV PDB
9.0 -0.3545 4.0982 View CSV PDB