AmyloComp

Predictor of co-aggregation of two proteins within an amyloid fibril.

It can be applied
(1) to predict a potential protein-protein interaction in the form of a common amyloid fibril,
(2) to assesses the likelihood of one protein inducing the amyloid formation of another,
(3) to test the hypothesis that certain bacteria or viruses may trigger amyloidosis in humans,
(4) to design an artificial amyloid fibrils composed of different proteins.

Reference fasta sequence :

NOTE : Maximum 10 000 characters

Example


Comparison fasta sequence :

NOTE : Maximum 10 000 characters

Example


Option :

Threshold :
Recommended values of ArchCandy score : 0.40 to 0.56


Sequence (Example):

NOTE : Maximum 10 000 characters

Proteome selection


AmyloComp - Documentation

Input
There are two options for the input:

  1. “Sequence vs sequence” To paste or download two protein sequences in FASTA format in different input windows.

    In addition, it is possible to establish a threshold of ArchCandy 2.0 score. ArchCandy searches for beta-arches in two input sequences to compare. Recommended values of the threshold are 0.40 to 0.56.

  2. “Sequence vs proteome"
    To paste or download a query protein sequences in FASTA format in the input window and to choose an organism in “Proteome selection”. At present, the human proteome is pre-selected as the most important for the analysis. In future, the other proteomes can be added.

    Attention! The proteome option is under development. Please, reanalyze the protein pairs of interest with the "Sequence vs sequence" option.

    “Jobs submitted” option allows to visualize previous jobs

Output

  1. “Sequence vs sequence”
    Output shows a Table with names of proteins; CS score; a probability to co-aggregate; positions of the regions that are involved in the co-aggregation ; "Area" that is involved in the co-aggregation; a fraction of Gln+Asn residues in the detected amyloid-forming regions; a fraction of apolar residues in the detected amyloid-forming regions; 2D structures of beta-arches within the co-aggregated fibrils.

    To visualize the 2D structures it is necessary to click on “Toggle Arch”. Values in the columns with titles in a blue color can be sorted by clicking on the title.

    The output can also be downloaded as a CSV file by clicking on “Download results”.

  2. “Sequence vs proteome"
    Output shows a Table with names of proteins; CS score; a probability to co-aggregate; positions of the regions that are involved in the co-aggregation; 2D structures of beta- arches within the co-aggregated fibrils.

    To visualize the 2D structures it is necessary to click on “Toggle Arch”. The scores and probabilities in the columns can be sorted by clicking on the title (blue color).

    The output can also be downloaded as a CSV file by clicking on “Download results”.


For more details, see Bondarev et al., “AmyloComp: a bioinformatic tool for prediction of amyloid co-aggregation” (submitted).