BetaSerpentine-1.0: a program for reconstruction of amyloid structures containing adjacent β-arches

Numerous studies suggest that amyloid forming regions of more than 30 residues evoke structural arrangements consisting of several adjacent β-arches called β-serpentines or superpleated β-structure (Kajava A.V. et al., 2010, FASEB J). The BetaSerpentine program searches for possible β-serpentines within a protein and output them in order of preference starting from the highest score.

N.B. BetaSerpentine program is not aimed at the detection of the amyloidogenic regions. If you want, first, to predict the amyloidogenicity of your protein, use ArchCandy.

A search of β-serpentines may take up to several minutes It takes approximately 10 seconds for short Amyloid-β peptide and up to 3-5 minutes for proteins with long amyloidogenic region like Sup35 or Ure2. after this you will be automatically redirected to the output page.


Attention :

  • As the input a plain protein sequence (minimal length is 18 amino acids) or FASTA format may be used (it is preferable to use FASTA format with Uniprot-like header; otherwise, protein name and additional information may be lost in the output).
  • In highly amyloidogenic and low complexity sequences the program can find thousands of β-serpentinesFor example, with default thresholds PrP has 819 β-serpentines, Sup35 and Ure2 proteins have 5828 and 7454, respectively. . Analysis of proteins with very big numbers of β-arches (for example, Rnq1) with default parameters will be interrupted because it will take several hours. To analyse them you should increase the β-arches threshold or try to analyse a part of the protein.
Please, cite:
Bondarev, Stanislav A, Olga V Bondareva, Galina A Zhouravleva, and Andrey V Kajava. “BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures.” Bioinformatics 34, no. 4 (2017): 599-608. doi: 10.1093/bioinformatics/btx629
Contacts: andrey.kajava@crbm.cnrs.fr, s.bondarev@spbu.ru

Paste a sequence in FASTA format or in plain text:

Min. length of protein sequence is 18 amino acids; max. length of input is 60.000 symbols
NOTE : One sequence per run
Example

Options :

Specify thresholdsDefault values for individual β-arches and β-serpentines thresholds are 0.0 and 0.2, respectively:




Similarity to consensus Score