Project name: GLP-1 7-37 amide

Status: done

Started: 2024-04-26 16:41:08
Chain sequence(s) B: GTFTSDVSSYLEGQAAKEFIAWLVRGR
input PDB
Selected Chain(s) B
Distance of aggregation 5 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]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with B chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[WARNING]    PDB-Info: The input structure is likely a peptide. Results may be inaccurate.         (00:00:01)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average 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                                          (00:00:11)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/302ed753bcb0ff0/tmp/folded.pdb                (00:00:11)
[INFO]       Main:     Simulation completed successfully.                                          (00:00:29)
Show buried residues
Minimal score value
-1.9623
Maximal score value
1.9281
Average score
0.0952
Total score value
2.4745
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
10 G B -0.4793
11 T B 0.1979
12 F B 1.9281
14 S B -0.4256
15 D B -0.7581
16 V B 1.6786
17 S B 0.0689
18 S B -0.0096
19 Y B 1.7450
20 L B 1.4594
21 E B -1.5625
22 G B -0.5349
23 Q B -0.5609
24 A B 0.0013
25 A B -0.2475
26 K B -1.9623
27 E B -1.2924
28 F B 1.6941
29 I B 1.8495
30 A B 0.3953
31 W B 1.4499
32 L B 0.8479
33 V B 1.5459
34 R B -1.6079
35 G B -1.0900
36 R B -1.8563
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 likely a peptide. Results may be inaccurate. The input structure is partially or entirely disordered. Average score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 0.3474 4.2194 View CSV PDB
4.5 0.3169 4.2194 View CSV PDB
5.0 0.2757 4.2194 View CSV PDB
5.5 0.2311 4.2194 View CSV PDB
6.0 0.1926 4.2194 View CSV PDB
6.5 0.167 4.2194 View CSV PDB
7.0 0.1572 4.2194 View CSV PDB
7.5 0.161 4.2194 View CSV PDB
8.0 0.1731 4.2194 View CSV PDB
8.5 0.1904 4.2194 View CSV PDB
9.0 0.2118 4.2194 View CSV PDB