AmyPro: a database of proteins with validated amyloidogenic regions.

TitleAmyPro: a database of proteins with validated amyloidogenic regions.
Publication TypeJournal Article
Year of Publication2018
AuthorsVaradi, M., G. De Baets, W. F. Vranken, P. Tompa, and R. Pancsa
JournalNucleic Acids Res
Volume46
IssueD1
PaginationD387-D392
Date Published2018 Jan 04
ISSN1362-4962
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.

DOI10.1093/nar/gkx950
Alternate JournalNucleic Acids Res.
PubMed ID29040693
PubMed Central IDPMC5753394
Grant ListMC_U105185859 / / Medical Research Council / United Kingdom
subject_category: 
Research group: