Project name: NilD_Rosetta

Status: done

submitted: 2020-06-19 21:00:15, status changed: 2020-06-24 01:25:57
Settings
Chain sequence(s) A: MFPVNTGINQTMATLNFLVYNSMFPVSTGIN
Distance of aggregation 10 Å
Dynamic mode Yes
Show buried residues

Minimal score value
-0.9591
Maximal score value
4.1084
Average score
1.8857
Total score value
58.4556

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
1 M A 2.1594
2 F A 2.7945
3 P A 1.7869
4 V A 2.5204
5 N A 1.1698
6 T A 0.5275
7 G A 0.6195
8 I A 1.3170
9 N A -0.5249
10 Q A -0.9591
11 T A 0.5115
12 M A 1.3067
13 A A 1.0515
14 T A 1.8410
15 L A 2.8888
16 N A 1.9268
17 F A 4.0038
18 L A 4.0375
19 V A 4.0161
20 Y A 4.1084
21 N A 3.0073
22 S A 2.5182
23 M A 3.5148
24 F A 3.7795
25 P A 1.8021
26 V A 2.7368
27 S A 1.6875
28 T A 1.0527
29 G A 0.6249
30 I A 1.1104
31 N A -0.4817

Above is the comparison between the input structure and the most aggregation prone model (predicted in the flexibility simulations, download both models in the PDB file format , download table with rmsd values ). The picture presents the most aggregation prone model (in blue) superimposed on the input structure (in red). The plot shows rmsd profile (distances between residues of the superimposed structures).

Dynamic mode uses CABS-flex simulations of protein structure fluctuations. The structure fluctuations may have impact on the size and extent of aggregation "hot-spots" on the protein surface. The dynamic mode uses the following pipeline: (1) based on the input structure, CABS-flex predicts a set of different models reflecting protein dynamics in solution; (2) for each of these models A3D score is calculated; (3) finally, the most aggregation prone model (the model with the highest A3D score, 1.8857 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015