Aggrescan3D: test

Project name: test_dyn

Status: done

submitted: 2018-11-24 14:36:07, status changed: 2018-11-24 14:54:57

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Chain sequence(s)	P: QPPVPPQRPM
Distance of aggregation	10 Å
Dynamic mode	Yes

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Show buried residues

Minimal score value: -2.386
Maximal score value: 1.2727
Average score: -0.6439
Total score value: -6.4385

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	Q	P	-1.1543
2	P	P	-0.4265
3	P	P	0.1011
4	V	P	1.2727
5	P	P	-0.0205
6	P	P	-0.9053
7	Q	P	-2.1824
8	R	P	-2.3860
9	P	P	-0.9020
10	M	P	0.1647

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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, -0.6439 in this case) is selected and presented in A3D results.