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Nucleic Acids Res. 2018 Jan 4;46(D1):D387-D392. doi: 10.1093/nar/gkx950.

AmyPro: a database of proteins with validated amyloidogenic regions.

Author information

1
Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
2
MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
3
Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, 1050, Belgium.
4
Interuniversity Institute of Bioinformatics in Brussels (IB) 2, ULB-VUB, Brussels, 1050, Belgium.
5
VIB Center for Structural Biology, Vrije Universiteit Brussel (VUB), Brussels, 1050, Belgium.
6
Institute of Enzymology, Research Centre for Natural Sciences of the HAS, Budapest, 1117, Hungary.

Abstract

Soluble functional proteins may transform into insoluble amyloid fibrils that deposit in a variety of tissues. Amyloid formation is a hallmark of age-related degenerative disorders. Perhaps surprisingly, amyloid fibrils can also be beneficial and are frequently exploited for diverse functional roles in organisms. Here we introduce AmyPro, an open-access database providing a comprehensive, carefully curated collection of validated amyloid fibril-forming proteins from all kingdoms of life classified into broad functional categories (http://amypro.net). In particular, AmyPro provides the boundaries of experimentally validated amyloidogenic sequence regions, short descriptions of the functional relevance of the proteins and their amyloid state, a list of the experimental techniques applied to study the amyloid state, important structural/functional/variation/mutation data transferred from UniProt, a list of relevant PDB structures categorized according to protein states, database cross-references and literature references. AmyPro greatly improves on similar currently available resources by incorporating both prions and functional amyloids in addition to pathogenic amyloids, and allows users to screen their sequences against the entire collection of validated amyloidogenic sequence fragments. By enabling further elucidation of the sequential determinants of amyloid fibril formation, we hope AmyPro will enhance the development of new methods for the precise prediction of amyloidogenic regions within proteins.

PMID:
29040693
PMCID:
PMC5753394
DOI:
10.1093/nar/gkx950
[Indexed for MEDLINE]
Free PMC Article

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