ArticleScientific reports2017
Amyloidogenic motifs revealed by n-gram analysis.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Assessment of Aggregation- and Condensation-Prone Regions of Proteins Involved in Neurodegenerative, Neurological and Mental-State Diseases.Biomolecules · 2026Article
- Bioinformatic assessment of the potential amyloidogenicity of the human and evolutionarily more ancient proteomes.The Biochemical journal · 2026Article
- Application of artificial intelligence for the prediction of amyloidoses.Neural regeneration research · 2026Article
- How far can you go? Extrapolating values of catalytic activity from known protein landscapes in natural and directed evolution.Chemical Society reviews · 2026Review
- Surface cues shape procoagulant properties of amyloidogenic microclots.Cell death & disease · 2026Review
- Aggregation in gut: on the link between neurodegeneration and bacterial functional amyloids.NPJ biofilms and microbiomes · 2026Article
- Experimentally validated deep learning control of protein aggregation.Communications chemistry · 2026Article
- Tau protein in Parkinson's disease: advances in phosphoproteomics and molecular dynamics simulations.Frontiers in aging neuroscience · 2026Review
- Uncovering the hidden biology of fibrinaloid microclot complexes in complex, inflammatory diseases.QRB discovery · 2026Review
- AmyloGram reveals amyloidogenic potential in stroke thrombus proteomes.The Biochemical journal · 2025Article
- Neurodegeneration Through the Lens of Bioinformatics Approaches: Computational Mechanisms of Protein Misfolding.International journal of molecular sciences · 2025Review
- A novel alpha-synuclein G14R missense variant is associated with atypical neuropathological features.Molecular neurodegeneration · 2025Article
- Employing deep mutational scanning in theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Comprehensive protein datasets and benchmarking for liquid-liquid phase separation studies.Genome biology · 2025Article
- A conserved motif in Henipavirus P/V/W proteins drives the fibrillation of the W protein from Hendra virus.Protein science : a publication of the Protein Society · 2025Article
- The Proteome Content of Blood Clots Observed Under Different Conditions: Successful Role in Predicting Clot Amyloid(ogenicity).Molecules (Basel, Switzerland) · 2025Review
- Prediction and Evaluation of Protein Aggregation with Computational Methods.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Proteomic Evidence for Amyloidogenic Cross-Seeding in Fibrinaloid Microclots.International journal of molecular sciences · 2024Article
- DOTAD: A Database of Therapeutic Antibody Developability.Interdisciplinary sciences, computational life sciences · 2024Article
- Photocontrolled Reversible Amyloid Fibril Formation of Parathyroid Hormone-Derived Peptides.Bioconjugate chemistry · 2024Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Amyloids are proteins associated with several clinical disorders, including Alzheimer's, and Creutzfeldt-Jakob's. Despite their diversity, all amyloid proteins can undergo aggregation initiated by short segments called hot spots. To find the patterns defining the hot spots, we trained predictors of amyloidogenicity, using n-grams and random forest classifiers. Since the amyloidogenicity may not depend on the exact sequence of amino acids but on their more general properties, we tested 524,284 reduced amino acid alphabets of different lengths (three to six letters) to find the alphabet providing the best performance in cross-validation. The predictor based on this alphabet, called AmyloGram, was benchmarked against the most popular tools for the detection of amyloid peptides using an external data set and obtained the highest values of performance measures (AUC: 0.90, MCC: 0.63). Our results showed sequential patterns in the amyloids which are strongly correlated with hydrophobicity, a tendency to form β-sheets, and lower flexibility of amino acid residues. Among the most informative n-grams of AmyloGram we identified 15 that were previously confirmed experimentally. AmyloGram is available as the web-server: http://smorfland.uni.wroc.pl/shiny/AmyloGram/ and as the R package AmyloGram. R scripts and data used to produce the results of this manuscript are available at http://github.com/michbur/AmyloGramAnalysis .
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