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Bioinformatics. 2018 Feb 15;34(4):599-608. doi: 10.1093/bioinformatics/btx629.

BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures.

Author information

1
Laboratory of Amyloid Biology and Department of Genetics and Biotechnology, St. Petersburg State University, Saint Petersburg 199034, Russia.
2
Laboratory of Molecular Systematics, Zoological Institute RAS, Saint Petersburg 199034, Russia.
3
Structural Bioinformatics and Molecular Modeling, Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier 34293, France.
4
Institut de Biologie Computationnelle, Montpellier 34095, France.
5
Bioengineering Department, University ITMO, Saint Petersburg, 197101, Russia.

Abstract

Motivation:

Numerous experimental studies have suggested that polypeptide chains of large amyloidogenic regions zig-zag in β-serpentine arrangements. These β-serpentines are stacked axially and form the superpleated β-structure. Despite this progress in the understanding of amyloid folds, the determination of their 3D structure at the atomic level is still a problem due to the polymorphism of these fibrils and incompleteness of experimental structural data. Today, the way to get insight into the atomic structure of amyloids is a combination of experimental studies with bioinformatics.

Results:

We developed a computer program BetaSerpentine that reconstructs β-serpentine arrangements from individual β-arches predicted by ArchCandy program and ranks them in order of preference. It was shown that the BetaSerpentine program in combination with the experimental data can be used to gain insight into the detailed 3D structure of amyloids. It opens avenues to the structure-based interpretation and design of the experiments.

Availability and implementation:

BetaSerpentine webserver can be accessed through website: http://bioinfo.montp.cnrs.fr/b-serpentine. Source code is available in git.hub repository (github.com/stanislavspbgu/BetaSerpentine).

Contact:

stanislavspbgu@gmail.com or andrey.kajava@crbm.cnrs.fr.

Supplementary information:

Supplementary data are available at Bioinformatics online.

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